Circulating neuron-derived cfDNA for blood-based detection of Alzheimer's and other neurodegenerative conditions.

Code ↔ Paper

4 matches between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

The 4 matches

[1] § Materials and methods › Differential methylation analysis and classifier development ↔ R/classify_ch3_reads.R, lines 56–159 · score 0.78 · collapse_windows, CpG position, mod diff, CH3, database, db
[2] § Materials and methods › Differential methylation analysis and classifier development ↔ R/collapse_ch3_windows.R, lines 38–130 · score 0.66 · collapse windows, mod diff, CH3, database, db
[3] § Materials and methods › DNA sequencing ↔ dorado/hts_utils/fastq_tags.cpp, lines 20–106 · score 0.64 · 400bps hac, dna r10, e8, dorado, basecalled, model
[4] § Materials and methods › DNA sequencing ↔ dorado/hts_utils/HeaderMapper.cpp, lines 471–530 · score 0.63 · 400bps hac, dna r10, e8, ONT

Paper

Loaded from Europe PMC by your browser, not stored by OSCR: doi.org · Europe PMC

The paper is loaded when this pane is shown.

The paper is loaded by your browser, with JavaScript: read it at doi.org or on Europe PMC.

The authors' code

R · 159 lines · 6.4 KB · other · 1 match

#' Classify Reads as Case or Control Based on Methylation Profiles
#'
#' This function classifies reads in the `reads` table of a DuckDB database
#' as either `"case"`, `"control"`, or `"unknown"` based on similarity
#' to reference methylation fractions in a `key_table` (e.g., a collapsed windows file).
#' Classification is based on how close the read's `mh_frac` is to the average
#' case or control `mh_frac`, within a user-defined `meth_diff_threshold`.
#'
#' @param ch3_db Path to a DuckDB `.db` file created by this package (e.g., from `summarize_reads()`).
#' @param table_name Character. Name of the output table to store classified reads (default: "classified_reads").
#' @param reads_table Character. Name of the reads table in which you want to classify the reads (default: "reads").
#' @param key_table Path to a CSV, TSV, or BED file generated by `collapse_windows()`. Must include the columns:
#' `chrom`, `start`, `end`, `avg_mh_frac_control`, `avg_mh_frac_case`, and `avg_meth_diff`.
#' @param case Character string used to label case reads (e.g., `"case"`).
#' @param control Character string used to label control reads (e.g., `"control"`).
#' @param meth_diff_threshold Numeric value specifying the maximum difference in `mh_frac` allowed
#' to match either case or control averages. Must be less than half the minimum absolute value of
#' `avg_meth_diff` to prevent ambiguous classifications.
#'
#' @return Invisibly returns the open database connection with a new table named `classified_reads`
#' added to the database. This table includes:
#' \itemize{
#' \item \code{sample_name} – Sample identifier
#' \item \code{read_id} – Unique read identifier
#' \item \code{first_cpg_pos} – First CpG position of the read
#' \item \code{last_cpg_pos} – Last CpG position of the read
#' \item \code{mh_frac} – Methylation fraction of the read
#' \item \code{classification} – `"case"`, `"control"`, or `"unknown"`
#' }
#'
#' @details
#' This function runs entirely in SQL for scalability. It performs an interval join
#' between the `reads` table and the key table on `chrom` and CpG position range,
#' then classifies each read based on proximity of `mh_frac` to either `avg_mh_frac_control` or `avg_mh_frac_case`.
#'
#' @examples
#' \dontrun{
#' classify_ch3_reads(
#' ch3_db = "my_data.ch3.db",
#' key_table = "key_table.csv",
#' case = "treated",
#' control = "untreated",
#' meth_diff_threshold = 0.1
#' )
#' }
#'
#' @importFrom DBI dbConnect dbDisconnect dbExistsTable dbExecute dbWriteTable
#' @importFrom duckdb duckdb
#' @importFrom readr read_csv read_tsv
#' @importFrom tools file_ext
#' @importFrom dplyr tbl
#' @importFrom glue glue
#'
#' @export
classify_ch3_reads <- function(ch3_db,
table_name = "classified_reads",
reads_table = "reads",
key_table,
case,
control,
meth_diff_threshold = 0.1) {
start_time <- Sys.time()
ch3_db <- .ch3helper_connectDB(ch3_db)
# Check if "mod_diff" table exists
if (!dbExistsTable(ch3_db$con, reads_table)) {
stop(glue("Error: Reads table not found in the database.
Please run 'summarize_reads()' on database first to generate it."))
}
# Read in key_table and make sure the key_table looks like collapsed_windows...
file_ext <- file_ext(key_table)
if (file_ext == "csv") {
annotation <- read_csv(key_table,
show_col_types = FALSE)
} else if (file_ext %in% c("bed", "tsv")) {
annotation <- read_tsv(key_table,
show_col_types = FALSE)
} else {
stop("Invalid file type. Only CSV, TSV, or BED files are supported.")
}
# Make sure key_table is a collapsed window format from collapse_windows().
required_cols <- c("chrom", "start", "end", "avg_mh_frac_control", "avg_mh_frac_case", "avg_meth_diff")
if (!all(required_cols %in% colnames(annotation))) {
stop("\nMissing one or more required columns: start, end, avg_mh_frac_control, avg_meth_diff.\nkey_table must be a collapsed_windows table from the function collapse_windows().")
}
# Check to make sure threshold, make sure it is less than 1/2 of min_diff... make sure threshold doesn't overlap
if (any(meth_diff_threshold >= abs(annotation$avg_meth_diff) / 2, na.rm = TRUE)) {
stop("`\nmeth_diff_threshold` must be less than half the absolute value of all `avg_meth_diff` values.\nThis is to avoid overlapping in classification.\n")
}
# Upload annotation as a temporary table
dbExecute(ch3_db$con, "DROP TABLE IF EXISTS temp_key_table;")
dbWriteTable(ch3_db$con, "temp_key_table", annotation, temporary = TRUE)
if (dbExistsTable(ch3_db$con, table_name))
dbRemoveTable(ch3_db$con, table_name)
query <- glue("
CREATE TABLE {table_name} AS
SELECT
r.sample_name,
r.read_id,
r.first_cpg_pos,
r.last_cpg_pos,
r.mh_frac,
CASE
WHEN ABS(r.mh_frac - k.avg_mh_frac_control) <= {meth_diff_threshold} THEN '{control}'
WHEN ABS(r.mh_frac - k.avg_mh_frac_case) <= {meth_diff_threshold} THEN '{case}'
ELSE 'unknown'
END AS classification
FROM
{reads_table} r
JOIN
temp_key_table k
ON
r.chrom = k.chrom
AND r.first_cpg_pos <= k.end
AND r.last_cpg_pos >= k.start")
dbExecute(ch3_db$con, query)
# Drop temporary tables
dbExecute(ch3_db$con, "DROP TABLE IF EXISTS temp_key_table;")
cat("\n")
end_time <- Sys.time()
total_time_difftime <- end_time - start_time
# Convert the total_time_difftime object to numeric seconds for a reliable comparison
total_seconds <- as.numeric(total_time_difftime, units = "secs")
if (total_seconds > 60) {
# If greater than 60 seconds, convert to numeric minutes for display
total_minutes <- as.numeric(total_time_difftime, units = "mins")
message("Classified reads table successfully created as '", table_name, "' in database!",
"\nTime elapsed: ", round(total_minutes, 2), " minutes\n")
} else {
# Otherwise, display in numeric seconds
message("Classified reads table successfully created as '", table_name, "' in database!",
"\nTime elapsed: ", round(total_seconds, 2), " seconds\n")
}
ch3_db$current_table = table_name
# print out table header for user
print(head(tbl(ch3_db$con, table_name)))
ch3_db <- .ch3helper_cleanup(ch3_db)
invisible(ch3_db)
}

classify_ch3_reads.R at commit 42977bd, under other · at the source

Overview

Authors: Chad Pollard^1,2, Ryan Miller^2,3, Isaac Stirland^1,2, Mykle Keni^1,2, Andrew Jenkins^1,2, Erin Saito², Jonathon T Hill^1,2, Tim Jenkins^1,2

Department of Cell Biology & Physiology, Brigham Young University, Provo, UT, United States
Resonant, LLC, Pleasant Grove, UT, United States
Department of Biology, Brigham Young University, Provo, UT, United States

Institutions: Brigham Young University (United States)

Journal: Frontiers in neurology, volume 17, article 1822479

Dates: received 3 March 2026; accepted 8 June 2026; published online 6 August 2026

Type: Research article · Language: English

License: CC BY

Identifiers: DOI 10.3389/fneur.2026.1822479 · PMID 42626456 · PMCID PMC13491437 · OpenAlex W7196980148

Open access: gold, a free copy (OpenAlex)

Status: code verified

Categories: genetics / omics (modality), other (modality), human (organism), other condition (population), Alzheimer's / dementia (population), clinical / translational (subfield)

Methods: Spectral & time-frequency, Statistics, Smoothing, state filtering, decompositions, Machine learning

Keywords: Alzheimer’s disease, blood biomarkers, cell-free DNA, liquid biopsy, methylation, mild cognitive impairment, neurodegeneration, precision medicine

MeSH: Alzheimer Disease*, Cell-Free Nucleic Acids*, Neurodegenerative Diseases*, Neurons*, Amyotrophic Lateral Sclerosis, Biomarkers, DNA Methylation, Female, Humans, Male (* major topic)

Topic: Single-cell and spatial transcriptomics (Molecular Biology, Biochemistry, Genetics and Molecular Biology), according to OpenAlex

Funding: Utah State University; Brigham Young University

Citations: not cited yet (Europe PMC); 97 references in the paper

Abstract

Blood-based biomarkers for neurodegenerative diseases are improving early detection and staging, but current assays primarily reflect aggregate neuropathology or generalized neuronal injury and do not resolve the specific neuronal populations affected. Circulating cell-free DNA (cfDNA) retains stable DNA methylation patterns reflective of tissue and cellular origin, making it a promising substrate for cell-of-origin analysis. However, conventional methylation approaches are limited by bisulfite-associated DNA damage and amplification-related bias, hindering the detection of neuron-derived cfDNA, a small fraction of total circulating cfDNA. Here, we present proof-of-concept evidence that native nanopore sequencing can support both brain methylation atlas generation and downstream cfDNA cell-of-origin classifier development in neurodegenerative disease. By directly profiling endogenous DNA methylation without bisulfite conversion or PCR amplification, nanopore sequencing preserves native molecules, reduces processing-related bias, and enables flexible, genome-wide methylation profiling that can be iteratively expanded as additional reference cell types are incorporated. Using whole-genome native nanopore sequencing, we generated a methylation reference atlas from six primary human neural cell populations—cortical neurons, dopaminergic neurons, spinal motor neurons, astrocytes, Schwann cells, and microglia—and developed cell-type-informed cfDNA classifiers. Classifier performance was assessed in silico using dilution series designed to model physiologic admixture. The framework was then applied to 137 blood plasma samples from individuals with mild cognitive impairment (MCI), Alzheimer’s disease (AD), Parkinson’s disease (PD), amyotrophic lateral sclerosis (ALS), and healthy controls. Elevated circulating cfDNA fragments exhibited methylation patterns similar to reference profiles from selectively vulnerable neuronal populations, including cortical neuron-like signatures in AD and progressive MCI, dopaminergic neuron-like signatures in PD, and spinal motor neuron-like signatures in ALS. Multivariate integration of neuronal signatures improved the separation of diagnostic groups within this cohort (AUC > 0.85). Although the reported atlas is limited and additional validation in larger and independent cohorts will be required, these results support the feasibility of native cfDNA nanopore methylation sequencing as a flexible platform for brain-derived cfDNA analysis and more cell-type-informed investigation of neurodegeneration from peripheral blood.

Reproduced under the paper's license (CC BY), from the paper cited above.

Repositories

Its files are read in the Code ↔ Paper reader above, with 4 matches between paragraphs and lines of code.

nanoporetech/dorado

License: GPL-3.0

State: the link answers, verified on 27 September 2026

Evidence: files inventoried

Commit: 8b8fc5d36a9c0baab262a743cb175b5878e38ca6, 26 August 2026

Languages: C++ (371), C/C++ (329), Python (34), Shell (16)

Size: 1,496 files, 750 scripts

Software Heritage: archived

Found in: the text

Holds: README, license file, environment (tetra/setup.py), tests, continuous integration

Not found: CITATION.cff, documentation

Tools: SAMtools (5 files), pandas (3 files), NumPy (2 files), Biopython (1 file), Matplotlib (1 file), pysam (1 file)

Availability: 1 check, the latest on 27 September 2026: the link answers

27 September 2026: the link answers

752 files

.gitlab/run_clang_tidy.sh, Shell, 115 lines
dorado/3rdparty/fake_cudnn/cudnn.h, C/C++, 1 line
dorado/3rdparty/fake_cudnn/cudnn_version.h, C/C++, 1 line
dorado/3rdparty/intervaltree/IntervalTree.h, C/C++, 346 lines
dorado/3rdparty/kadayashi/include/bam_record_parsing.h, C/C++, 34 lines
dorado/3rdparty/kadayashi/include/blocked_bloom_filter.h, C/C++, 34 lines
dorado/3rdparty/kadayashi/include/faidx_utils.h, C/C++, 17 lines
dorado/3rdparty/kadayashi/include/hts_types.h, C/C++, 46 lines
dorado/3rdparty/kadayashi/include/local_haplotagging.h, C/C++, 501 lines
dorado/3rdparty/kadayashi/include/sequence_utility.h, C/C++, 15 lines
dorado/3rdparty/kadayashi/include/types.h, C/C++, 182 lines
dorado/3rdparty/kadayashi/src/bam_tagging.cpp, C++, 255 lines
dorado/3rdparty/kadayashi/src/bam_tagging.h, C/C++, 34 lines
dorado/3rdparty/kadayashi/src/cli.cpp, C++, 823 lines
dorado/3rdparty/kadayashi/src/cli.h, C/C++, 117 lines
dorado/3rdparty/kadayashi/src/haplotag_lib/bam_record_parsing.cpp, C++, 296 lines
dorado/3rdparty/kadayashi/src/haplotag_lib/blocked_bloom_filter.cpp, C++, 87 lines
dorado/3rdparty/kadayashi/src/haplotag_lib/faidx_utils.cpp, C++, 62 lines
dorado/3rdparty/kadayashi/src/haplotag_lib/hts_types.cpp, C++, 22 lines
dorado/3rdparty/kadayashi/src/haplotag_lib/local_haplotagging.cpp, C++, 3,895 lines
dorado/3rdparty/kadayashi/src/haplotag_lib/sequence_utility.cpp, C++, 44 lines
dorado/3rdparty/kadayashi/src/haplotag_lib/string_utils.cpp, C++, 84 lines
dorado/3rdparty/kadayashi/src/haplotag_lib/string_utils.h, C/C++, 31 lines
dorado/3rdparty/kadayashi/src/haplotag_lib/variant_graph.cpp, C++, 1,234 lines
dorado/3rdparty/kadayashi/src/haplotag_lib/variant_graph.h, C/C++, 23 lines
dorado/3rdparty/kadayashi/src/kadayashi_utils.cpp, C++, 354 lines
dorado/3rdparty/kadayashi/src/kadayashi_utils.h, C/C++, 20 lines
dorado/3rdparty/kadayashi/src/ketopt.h, C/C++, 149 lines
dorado/3rdparty/kadayashi/src/main.cpp, C++, 334 lines
dorado/3rdparty/kadayashi/src/pipeline.cpp, C++, 2,414 lines
dorado/3rdparty/kadayashi/src/pipeline.h, C/C++, 84 lines
dorado/3rdparty/kadayashi/src/resources.cpp, C++, 32 lines
dorado/3rdparty/kadayashi/src/resources.h, C/C++, 11 lines
dorado/aligner/Minimap2Aligner.cpp, C++, 675 lines
dorado/aligner/include/aligner/Minimap2Aligner.h, C/C++, 54 lines
dorado/alignment/BedFileAccess.cpp, C++, 31 lines
dorado/alignment/IndexFileAccess.cpp, C++, 146 lines
dorado/alignment/Minimap2Index.cpp, C++, 319 lines
dorado/alignment/Minimap2MemoryLimiter.cpp, C++, 103 lines
dorado/alignment/Minimap2Options.cpp, C++, 101 lines
dorado/alignment/bed_file.cpp, C++, 255 lines
dorado/alignment/include/alignment/BedFileAccess.h, C/C++, 26 lines
dorado/alignment/include/alignment/IndexFileAccess.h, C/C++, 73 lines
dorado/alignment/include/alignment/Minimap2Index.h, C/C++, 70 lines
dorado/alignment/include/alignment/Minimap2IndexSupportTypes.h, C/C++, 17 lines
dorado/alignment/include/alignment/Minimap2MemoryLimiter.h, C/C++, 23 lines
dorado/alignment/include/alignment/Minimap2Options.h, C/C++, 52 lines
dorado/alignment/include/alignment/alignment_info.h, C/C++, 16 lines
dorado/alignment/include/alignment/bed_file.h, C/C++, 44 lines
dorado/alignment/include/alignment/minimap2_args.h, C/C++, 50 lines
dorado/alignment/include/alignment/minimap2_wrappers.h, C/C++, 33 lines
dorado/alignment/include/alignment/sam_utils.h, C/C++, 14 lines
dorado/alignment/minimap2_args.cpp, C++, 334 lines
dorado/alignment/sam_utils.cpp, C++, 305 lines
dorado/api/caller_creation.cpp, C++, 34 lines
dorado/api/include/api/caller_creation.h, C/C++, 45 lines
dorado/api/include/api/pipeline_creation.h, C/C++, 60 lines
dorado/api/include/api/runner_creation.h, C/C++, 42 lines
dorado/api/pipeline_creation.cpp, C++, 198 lines
dorado/api/runner_creation.cpp, C++, 214 lines
dorado/basecall/ChunkBenchmarks.cpp, C++, 57 lines
dorado/basecall/ChunkBenchmarks.h, C/C++, 46 lines
dorado/basecall/CudaCaller.cpp, C++, 762 lines
dorado/basecall/CudaModelRunner.cpp, C++, 92 lines
dorado/basecall/MetalModelRunner.cpp, C++, 47 lines
dorado/basecall/ModelRunner.cpp, C++, 57 lines
dorado/basecall/ModelRunnerBase.cpp, C++, 10 lines
dorado/basecall/caller/MPSCaller.cpp, C++, 260 lines
dorado/basecall/caller/MPSCaller.h, C/C++, 35 lines
dorado/basecall/caller/MetalCaller.cpp, C++, 234 lines
dorado/basecall/caller/MetalCallerTask.h, C/C++, 23 lines
dorado/basecall/caller/MetalLSTMCaller.cpp, C++, 313 lines
dorado/basecall/caller/MetalLSTMCaller.h, C/C++, 56 lines
dorado/basecall/crf_utils.cpp, C++, 250 lines
dorado/basecall/decode/CPUDecoder.cpp, C++, 158 lines
dorado/basecall/decode/CPUDecoder.h, C/C++, 24 lines
dorado/basecall/decode/CUDADecoder.cpp, C++, 197 lines
dorado/basecall/decode/CUDADecoder.h, C/C++, 25 lines
dorado/basecall/decode/Decoder.cpp, C++, 31 lines
dorado/basecall/decode/Decoder.h, C/C++, 36 lines
dorado/basecall/decode/beam_search.cpp, C++, 608 lines
dorado/basecall/decode/beam_search.h, C/C++, 22 lines
dorado/basecall/include/basecall/CudaCaller.h, C/C++, 113 lines
dorado/basecall/include/basecall/CudaModelRunner.h, C/C++, 51 lines
dorado/basecall/include/basecall/DecodedChunk.h, C/C++, 25 lines
dorado/basecall/include/basecall/MetalCaller.h, C/C++, 76 lines
dorado/basecall/include/basecall/MetalModelRunner.h, C/C++, 42 lines
dorado/basecall/include/basecall/ModelRunner.h, C/C++, 47 lines
dorado/basecall/include/basecall/ModelRunnerBase.h, C/C++, 52 lines
dorado/basecall/include/basecall/crf_utils.h, C/C++, 20 lines
dorado/basecall/model/CRFModel.cpp, C++, 148 lines
dorado/basecall/model/CRFModel.h, C/C++, 39 lines
dorado/basecall/model/MetalCRFModel.cpp, C++, 36 lines
dorado/basecall/model/MetalCRFModel.h, C/C++, 34 lines
dorado/basecall/model/TxModel.cpp, C++, 50 lines
dorado/basecall/model/TxModel.h, C/C++, 44 lines
dorado/batchsize_benchmarks/BenchmarkCache.cpp, C++, 155 lines
dorado/batchsize_benchmarks/BenchmarkCache.h, C/C++, 69 lines
dorado/batchsize_benchmarks/BenchmarkSink.cpp, C++, 49 lines
dorado/batchsize_benchmarks/BenchmarkSink.h, C/C++, 41 lines
dorado/batchsize_benchmarks/SpeedEntry.h, C/C++, 13 lines
dorado/batchsize_benchmarks/batchsize_benchmarks.cpp, C++, 291 lines
dorado/batchsize_benchmarks/batchsize_helpers.cpp, C++, 76 lines
dorado/batchsize_benchmarks/batchsize_helpers.h, C/C++, 14 lines
dorado/batchsize_benchmarks/compiled_timings.h, C/C++, 30 lines
dorado/batchsize_benchmarks/csv_helpers.cpp, C++, 74 lines
dorado/batchsize_benchmarks/csv_helpers.h, C/C++, 44 lines
dorado/batchsize_benchmarks/generate_chunk_auto_batchsize_benchmarks.sh, Shell, 35 lines
dorado/batchsize_benchmarks/include/batchsize_benchmarks/batchsize_benchmarks.h, C/C++, 37 lines
dorado/batchsize_benchmarks/tests/entries_equal.h, C/C++, 24 lines
dorado/batchsize_benchmarks/tests/test_batchsize_helpers.cpp, C++, 140 lines
dorado/batchsize_benchmarks/tests/test_cache.cpp, C++, 156 lines
dorado/batchsize_benchmarks/tests/test_csv.cpp, C++, 98 lines
dorado/cli/cli_lib/CorrectionAligner.h, C/C++, 28 lines
dorado/cli/cli_lib/CorrectionMapper.cpp, C++, 378 lines
dorado/cli/cli_lib/CorrectionMapper.h, C/C++, 94 lines
dorado/cli/cli_lib/CorrectionPafReader.cpp, C++, 93 lines
dorado/cli/cli_lib/CorrectionPafReader.h, C/C++, 30 lines
dorado/cli/cli_lib/CorrectionProgressTracker.cpp, C++, 118 lines
dorado/cli/cli_lib/CorrectionProgressTracker.h, C/C++, 34 lines
dorado/cli/cli_lib/ProgressTracker.cpp, C++, 290 lines
dorado/cli/cli_lib/ProgressTracker.h, C/C++, 94 lines
dorado/cli/cli_lib/SimpleProgressBar.h, C/C++, 53 lines
dorado/cli/cli_lib/aligner.cpp, C++, 410 lines
dorado/cli/cli_lib/basecall_output_args.cpp, C++, 133 lines
dorado/cli/cli_lib/basecall_output_args.h, C/C++, 33 lines
dorado/cli/cli_lib/basecaller.cpp, C++, 1,206 lines
dorado/cli/cli_lib/correct.cpp, C++, 576 lines
dorado/cli/cli_lib/demux.cpp, C++, 410 lines
dorado/cli/cli_lib/download.cpp, C++, 227 lines
dorado/cli/cli_lib/duplex.cpp, C++, 696 lines
dorado/cli/cli_lib/include/cli/cli.h, C/C++, 16 lines
dorado/cli/cli_lib/include/cli/utils/cli_utils.h, C/C++, 267 lines
dorado/cli/cli_lib/polish.cpp, C++, 1,331 lines
dorado/cli/cli_lib/polish_progress_tracker.cpp, C++, 58 lines
dorado/cli/cli_lib/polish_progress_tracker.h, C/C++, 30 lines
dorado/cli/cli_lib/read_output_progress_stats.cpp, C++, 375 lines
dorado/cli/cli_lib/read_output_progress_stats.h, C/C++, 101 lines
dorado/cli/cli_lib/smallvar.cpp, C++, 1,517 lines
dorado/cli/cli_lib/smallvar_progress_tracker.cpp, C++, 60 lines
dorado/cli/cli_lib/smallvar_progress_tracker.h, C/C++, 30 lines
dorado/cli/cli_lib/summary.cpp, C++, 124 lines
dorado/cli/cli_lib/summary_info.cpp, C++, 91 lines
dorado/cli/cli_lib/summary_info.h, C/C++, 15 lines
dorado/cli/cli_lib/trim.cpp, C++, 240 lines
dorado/cli/main.cpp, C++, 138 lines
dorado/compat/compat_utils.cpp, C++, 39 lines
dorado/compat/include/compat/compat_utils.h, C/C++, 19 lines
dorado/config/BasecallModelConfig.cpp, C++, 669 lines
dorado/config/BatchParams.cpp, C++, 118 lines
dorado/config/ModBaseBatchParams.cpp, C++, 77 lines
dorado/config/ModBaseModelConfig.cpp, C++, 584 lines
dorado/config/common.cpp, C++, 97 lines
dorado/config/include/config/BasecallModelConfig.h, C/C++, 179 lines
dorado/config/include/config/BatchParams.h, C/C++, 78 lines
dorado/config/include/config/ModBaseBatchParams.h, C/C++, 21 lines
dorado/config/include/config/ModBaseModelConfig.h, C/C++, 157 lines
dorado/config/include/config/common.h, C/C++, 59 lines
dorado/correct/conversions.cpp, C++, 43 lines
dorado/correct/decode.cpp, C++, 136 lines
dorado/correct/features.cpp, C++, 504 lines
dorado/correct/include/correct/conversions.h, C/C++, 18 lines
dorado/correct/include/correct/decode.h, C/C++, 12 lines
dorado/correct/include/correct/features.h, C/C++, 21 lines
dorado/correct/include/correct/infer.h, C/C++, 62 lines
dorado/correct/include/correct/types.h, C/C++, 69 lines
dorado/correct/include/correct/windows.h, C/C++, 93 lines
dorado/correct/infer.cpp, C++, 84 lines
dorado/correct/types.cpp, C++, 42 lines
dorado/correct/windows.cpp, C++, 832 lines
dorado/cudnn_dummy.cpp, C++, 1 line
dorado/data_loader/DataLoader.cpp, C++, 654 lines
dorado/data_loader/include/data_loader/DataLoader.h, C/C++, 94 lines
dorado/demux/AdapterDetector.cpp, C++, 371 lines
dorado/demux/AdapterDetectorSelector.cpp, C++, 25 lines
dorado/demux/BarcodeClassifier.cpp, C++, 1,602 lines
dorado/demux/BarcodeClassifierSelector.cpp, C++, 26 lines
dorado/demux/KitInfoProvider.cpp, C++, 30 lines
dorado/demux/Trimmer.cpp, C++, 314 lines
dorado/demux/adapter_info.cpp, C++, 64 lines
dorado/demux/adapter_primer_kits.cpp, C++, 352 lines
dorado/demux/adapter_primer_kits.h, C/C++, 68 lines
dorado/demux/include/demux/AdapterDetector.h, C/C++, 66 lines
dorado/demux/include/demux/AdapterDetectorSelector.h, C/C++, 21 lines
dorado/demux/include/demux/BarcodeClassifier.h, C/C++, 70 lines
dorado/demux/include/demux/BarcodeClassifierSelector.h, C/C++, 21 lines
dorado/demux/include/demux/KitInfoProvider.h, C/C++, 24 lines
dorado/demux/include/demux/Trimmer.h, C/C++, 23 lines
dorado/demux/include/demux/adapter_info.h, C/C++, 33 lines
dorado/demux/include/demux/barcoding_info.h, C/C++, 18 lines
dorado/demux/include/demux/parse_custom_kit.h, C/C++, 26 lines
dorado/demux/include/demux/parse_custom_sequences.h, C/C++, 20 lines
dorado/demux/parse_custom_kit.cpp, C++, 313 lines
dorado/demux/parse_custom_sequences.cpp, C++, 38 lines
dorado/devtools/slow_interpose.cpp, C++, 126 lines
dorado/devtools/slow_interpose.h, C/C++, 15 lines
dorado/file_info/file_info.cpp, C++, 335 lines
dorado/file_info/include/file_info/file_info.h, C/C++, 35 lines
dorado/hts_utils/FastxRandomReader.cpp, C++, 110 lines
dorado/hts_utils/FastxSequentialReader.cpp, C++, 66 lines
dorado/hts_utils/HeaderMapper.cpp, C++, 607 lines, 1 match
dorado/hts_utils/KString.cpp, C++, 42 lines
dorado/hts_utils/MergeHeaders.cpp, C++, 377 lines
dorado/hts_utils/bam_utils.cpp, C++, 611 lines
dorado/hts_utils/fai_utils.cpp, C++, 82 lines
dorado/hts_utils/fastq_tags.cpp, C++, 108 lines, 1 match
dorado/hts_utils/header_sq_record.cpp, C++, 66 lines
dorado/hts_utils/header_utils.cpp, C++, 115 lines
dorado/hts_utils/hts_file.cpp, C++, 652 lines
dorado/hts_utils/hts_types.cpp, C++, 99 lines
dorado/hts_utils/include/hts_utils/FastxRandomReader.h, C/C++, 40 lines
dorado/hts_utils/include/hts_utils/FastxSequentialReader.h, C/C++, 34 lines
dorado/hts_utils/include/hts_utils/HeaderMapper.h, C/C++, 104 lines
dorado/hts_utils/include/hts_utils/KString.h, C/C++, 61 lines
dorado/hts_utils/include/hts_utils/MergeHeaders.h, C/C++, 199 lines
dorado/hts_utils/include/hts_utils/bam_utils.h, C/C++, 299 lines
dorado/hts_utils/include/hts_utils/fai_utils.h, C/C++, 20 lines
dorado/hts_utils/include/hts_utils/fastq_tags.h, C/C++, 18 lines
dorado/hts_utils/include/hts_utils/header_sq_record.h, C/C++, 43 lines
dorado/hts_utils/include/hts_utils/header_utils.h, C/C++, 40 lines
dorado/hts_utils/include/hts_utils/hts_file.h, C/C++, 107 lines
dorado/hts_utils/include/hts_utils/hts_types.h, C/C++, 276 lines
dorado/hts_utils/include/hts_utils/sequence_file_format.h, C/C++, 18 lines
dorado/hts_utils/sequence_file_format.cpp, C++, 40 lines
dorado/hts_writer/HtsFileWriter.cpp, C++, 162 lines
dorado/hts_writer/HtsFileWriterBuilder.cpp, C++, 175 lines
dorado/hts_writer/StreamHtsFileWriter.cpp, C++, 66 lines
dorado/hts_writer/Structure.cpp, C++, 182 lines
dorado/hts_writer/StructuredHtsFileWriter.cpp, C++, 101 lines
dorado/hts_writer/SummaryFileWriter.cpp, C++, 444 lines
dorado/hts_writer/hts_writer_utils.h, C/C++, 35 lines
dorado/hts_writer/include/hts_writer/HtsFileWriter.h, C/C++, 87 lines
dorado/hts_writer/include/hts_writer/HtsFileWriterBuilder.h, C/C++, 86 lines
dorado/hts_writer/include/hts_writer/StreamHtsFileWriter.h, C/C++, 34 lines
dorado/hts_writer/include/hts_writer/Structure.h, C/C++, 97 lines
dorado/hts_writer/include/hts_writer/StructuredHtsFileWriter.h, C/C++, 34 lines
dorado/hts_writer/include/hts_writer/SummaryFileWriter.h, C/C++, 58 lines
dorado/hts_writer/include/hts_writer/interface.h, C/C++, 48 lines
dorado/metal-cpp-impl.cpp, C++, 6 lines
dorado/modbase/ModBaseCaller.cpp, C++, 277 lines
dorado/modbase/ModBaseContext.cpp, C++, 155 lines
dorado/modbase/ModBaseEncoder.cpp, C++, 140 lines
dorado/modbase/ModBaseRunner.cpp, C++, 157 lines
dorado/modbase/ModBaseScaler.cpp, C++, 105 lines
dorado/modbase/ModBaseScaler.h, C/C++, 67 lines
dorado/modbase/MotifMatcher.cpp, C++, 79 lines
dorado/modbase/encode_kmer.cpp, C++, 303 lines
dorado/modbase/include/modbase/ModBaseCaller.h, C/C++, 101 lines
dorado/modbase/include/modbase/ModBaseContext.h, C/C++, 99 lines
dorado/modbase/include/modbase/ModBaseEncoder.h, C/C++, 73 lines
dorado/modbase/include/modbase/ModBaseRunner.h, C/C++, 76 lines
dorado/modbase/include/modbase/MotifMatcher.h, C/C++, 25 lines
dorado/modbase/include/modbase/encode_kmer.h, C/C++, 21 lines
dorado/modbase/nn/ModBaseModel.cpp, C++, 670 lines
dorado/modbase/nn/ModBaseModel.h, C/C++, 20 lines
dorado/model_downloader/downloader.cpp, C++, 295 lines
dorado/model_downloader/downloader.h, C/C++, 43 lines
dorado/model_downloader/include/model_downloader/model_downloader.h, C/C++, 59 lines
dorado/model_downloader/model_downloader.cpp, C++, 103 lines
dorado/model_resolver/ModelResolver.cpp, C++, 437 lines
dorado/model_resolver/ModelSources.cpp, C++, 119 lines
dorado/model_resolver/Models.cpp, C++, 134 lines
dorado/model_resolver/include/model_resolver/ModelResolver.h, C/C++, 93 lines
dorado/model_resolver/include/model_resolver/ModelSources.h, C/C++, 39 lines
dorado/model_resolver/include/model_resolver/Models.h, C/C++, 65 lines
dorado/models/include/models/kits.h, C/C++, 266 lines
dorado/models/include/models/metadata.h, C/C++, 107 lines
dorado/models/include/models/model_complex.h, C/C++, 118 lines
dorado/models/include/models/models.h, C/C++, 105 lines
dorado/models/kits.cpp, C++, 480 lines
dorado/models/metadata.cpp, C++, 178 lines
dorado/models/model_complex.cpp, C++, 307 lines
dorado/models/models.cpp, C++, 2,323 lines
dorado/nn/AuxiliaryData.cpp, C++, 158 lines
dorado/nn/CRFModules.cpp, C++, 135 lines
dorado/nn/ConvStack.cpp, C++, 462 lines
dorado/nn/FLSTMStack.cpp, C++, 300 lines
dorado/nn/FactorisedLinearLayer.cpp, C++, 111 lines
dorado/nn/KoiThreads.cpp, C++, 25 lines
dorado/nn/KoiUtils.cpp, C++, 43 lines
dorado/nn/LSTMStack.cpp, C++, 247 lines
dorado/nn/LinearUpsample.cpp, C++, 25 lines
dorado/nn/MetalModules.cpp, C++, 565 lines
dorado/nn/RMSNorm.cpp, C++, 19 lines
dorado/nn/TxModules.cpp, C++, 960 lines
dorado/nn/WorkingMemory.cpp, C++, 116 lines
dorado/nn/include/nn/AuxiliaryData.h, C/C++, 93 lines
dorado/nn/include/nn/CRFModules.h, C/C++, 39 lines
dorado/nn/include/nn/ConvStack.h, C/C++, 58 lines
dorado/nn/include/nn/FLSTMStack.h, C/C++, 59 lines
dorado/nn/include/nn/FactorisedLinearLayer.h, C/C++, 42 lines
dorado/nn/include/nn/KoiThreads.h, C/C++, 23 lines
dorado/nn/include/nn/KoiUtils.h, C/C++, 13 lines
dorado/nn/include/nn/LSTMStack.h, C/C++, 40 lines
dorado/nn/include/nn/LinearLayer.h, C/C++, 21 lines
dorado/nn/include/nn/LinearUpsample.h, C/C++, 23 lines
dorado/nn/include/nn/MetalModules.h, C/C++, 86 lines
dorado/nn/include/nn/RMSNorm.h, C/C++, 19 lines
dorado/nn/include/nn/RNNStack.h, C/C++, 21 lines
dorado/nn/include/nn/TxModules.h, C/C++, 147 lines
dorado/nn/include/nn/WorkingMemory.h, C/C++, 84 lines
dorado/polish/include/polish/decode_data.h, C/C++, 21 lines
dorado/polish/include/polish/inference_data.h, C/C++, 20 lines
dorado/polish/include/polish/polish_impl.h, C/C++, 170 lines
dorado/polish/include/polish/polisher_resources.h, C/C++, 23 lines
dorado/polish/polish_impl.cpp, C++, 1,823 lines
dorado/poly_tail/dna_poly_tail_calculator.cpp, C++, 106 lines
dorado/poly_tail/dna_poly_tail_calculator.h, C/C++, 29 lines
dorado/poly_tail/include/poly_tail/poly_tail_calculator.h, C/C++, 105 lines
dorado/poly_tail/include/poly_tail/poly_tail_calculator_selector.h, C/C++, 43 lines
dorado/poly_tail/include/poly_tail/poly_tail_config.h, C/C++, 39 lines
dorado/poly_tail/plasmid_poly_tail_calculator.cpp, C++, 120 lines
dorado/poly_tail/plasmid_poly_tail_calculator.h, C/C++, 15 lines
dorado/poly_tail/poly_tail_calculator.cpp, C++, 361 lines
dorado/poly_tail/poly_tail_calculator_selector.cpp, C++, 85 lines
dorado/poly_tail/poly_tail_config.cpp, C++, 159 lines
dorado/poly_tail/rna_poly_tail_calculator.cpp, C++, 128 lines
dorado/poly_tail/rna_poly_tail_calculator.h, C/C++, 30 lines
dorado/read_pipeline/base/HtsReader.cpp, C++, 214 lines
dorado/read_pipeline/base/MessageSink.cpp, C++, 77 lines
dorado/read_pipeline/base/ReadInitialiser.cpp, C++, 155 lines
dorado/read_pipeline/base/ReadPipeline.cpp, C++, 165 lines
dorado/read_pipeline/base/chunk.cpp, C++, 152 lines
dorado/read_pipeline/base/include/read_pipeline/base/ClientInfo.h, C/C++, 20 lines
dorado/read_pipeline/base/include/read_pipeline/base/DefaultClientInfo.h, C/C++, 26 lines
dorado/read_pipeline/base/include/read_pipeline/base/HtsReader.h, C/C++, 149 lines
dorado/read_pipeline/base/include/read_pipeline/base/MessageSink.h, C/C++, 101 lines
dorado/read_pipeline/base/include/read_pipeline/base/ReadInitialiser.h, C/C++, 32 lines
dorado/read_pipeline/base/include/read_pipeline/base/ReadPipeline.h, C/C++, 124 lines
dorado/read_pipeline/base/include/read_pipeline/base/SimpleExecutor.h, C/C++, 36 lines
dorado/read_pipeline/base/include/read_pipeline/base/chunk.h, C/C++, 32 lines
dorado/read_pipeline/base/include/read_pipeline/base/messages.h, C/C++, 93 lines
dorado/read_pipeline/base/include/read_pipeline/base/messages/CorrectionAlignments.h, C/C++, 68 lines
dorado/read_pipeline/base/include/read_pipeline/base/messages/DuplexRead.h, C/C++, 38 lines
dorado/read_pipeline/base/include/read_pipeline/base/messages/ReadCommon.h, C/C++, 164 lines
dorado/read_pipeline/base/include/read_pipeline/base/messages/ReadPair.h, C/C++, 26 lines
dorado/read_pipeline/base/include/read_pipeline/base/messages/SimplexRead.h, C/C++, 48 lines
dorado/read_pipeline/base/include/read_pipeline/base/read_utils.h, C/C++, 18 lines
dorado/read_pipeline/base/include/read_pipeline/base/stitch.h, C/C++, 37 lines
dorado/read_pipeline/base/include/read_pipeline/base/terminate_options.h, C/C++, 15 lines
dorado/read_pipeline/base/messages.cpp, C++, 526 lines
dorado/read_pipeline/base/read_utils.cpp, C++, 168 lines
dorado/read_pipeline/base/stereo_features.cpp, C++, 226 lines
dorado/read_pipeline/base/stereo_features.h, C/C++, 12 lines
dorado/read_pipeline/base/stitch.cpp, C++, 110 lines
dorado/read_pipeline/base/tests/ReadInitialiserTest.cpp, C++, 146 lines
dorado/read_pipeline/nodes/AdapterDetectorNode.cpp, C++, 198 lines
dorado/read_pipeline/nodes/AlignerNode.cpp, C++, 257 lines
dorado/read_pipeline/nodes/BarcodeClassifierNode.cpp, C++, 239 lines
dorado/read_pipeline/nodes/BaseSpaceDuplexCallerNode.cpp, C++, 222 lines
dorado/read_pipeline/nodes/BasecallerNode.cpp, C++, 656 lines
dorado/read_pipeline/nodes/CorrectionInferenceNode.cpp, C++, 584 lines
dorado/read_pipeline/nodes/CorrectionPafWriterNode.cpp, C++, 43 lines
dorado/read_pipeline/nodes/DuplexReadTaggingNode.cpp, C++, 118 lines
dorado/read_pipeline/nodes/HtsWriterNode.cpp, C++, 146 lines
dorado/read_pipeline/nodes/ModBaseCallerNode.cpp, C++, 621 lines
dorado/read_pipeline/nodes/ModBaseChunkCallerNode.cpp, C++, 1,243 lines
dorado/read_pipeline/nodes/NullNode.cpp, C++, 24 lines
dorado/read_pipeline/nodes/PairingNode.cpp, C++, 549 lines
dorado/read_pipeline/nodes/PolyACalculatorNode.cpp, C++, 128 lines
dorado/read_pipeline/nodes/ReadFilterNode.cpp, C++, 73 lines
dorado/read_pipeline/nodes/ReadForwarderNode.cpp, C++, 33 lines
dorado/read_pipeline/nodes/ReadSplitNode.cpp, C++, 96 lines
dorado/read_pipeline/nodes/ReadToBamTypeNode.cpp, C++, 104 lines
dorado/read_pipeline/nodes/ScalerNode.cpp, C++, 292 lines
dorado/read_pipeline/nodes/StereoDuplexEncoderNode.cpp, C++, 138 lines
dorado/read_pipeline/nodes/SubreadTaggerNode.cpp, C++, 146 lines
dorado/read_pipeline/nodes/TrimmerNode.cpp, C++, 165 lines
dorado/read_pipeline/nodes/WriterNode.cpp, C++, 77 lines
dorado/read_pipeline/nodes/include/read_pipeline/nodes/AdapterDetectorNode.h, C/C++, 37 lines
dorado/read_pipeline/nodes/include/read_pipeline/nodes/AlignerNode.h, C/C++, 69 lines
dorado/read_pipeline/nodes/include/read_pipeline/nodes/BarcodeClassifierNode.h, C/C++, 50 lines
dorado/read_pipeline/nodes/include/read_pipeline/nodes/BaseSpaceDuplexCallerNode.h, C/C++, 35 lines
dorado/read_pipeline/nodes/include/read_pipeline/nodes/BasecallerNode.h, C/C++, 109 lines
dorado/read_pipeline/nodes/include/read_pipeline/nodes/CorrectionInferenceNode.h, C/C++, 70 lines
dorado/read_pipeline/nodes/include/read_pipeline/nodes/CorrectionPafWriterNode.h, C/C++, 20 lines
dorado/read_pipeline/nodes/include/read_pipeline/nodes/DuplexReadTaggingNode.h, C/C++, 32 lines
dorado/read_pipeline/nodes/include/read_pipeline/nodes/HtsWriterNode.h, C/C++, 46 lines
dorado/read_pipeline/nodes/include/read_pipeline/nodes/ModBaseCallerNode.h, C/C++, 94 lines
dorado/read_pipeline/nodes/include/read_pipeline/nodes/ModBaseChunkCallerNode.h, C/C++, 183 lines
dorado/read_pipeline/nodes/include/read_pipeline/nodes/NullNode.h, C/C++, 21 lines
dorado/read_pipeline/nodes/include/read_pipeline/nodes/PairingNode.h, C/C++, 126 lines
dorado/read_pipeline/nodes/include/read_pipeline/nodes/PolyACalculatorNode.h, C/C++, 42 lines
dorado/read_pipeline/nodes/include/read_pipeline/nodes/ReadFilterNode.h, C/C++, 40 lines
dorado/read_pipeline/nodes/include/read_pipeline/nodes/ReadForwarderNode.h, C/C++, 28 lines
dorado/read_pipeline/nodes/include/read_pipeline/nodes/ReadSplitNode.h, C/C++, 39 lines
dorado/read_pipeline/nodes/include/read_pipeline/nodes/ReadToBamTypeNode.h, C/C++, 36 lines
dorado/read_pipeline/nodes/include/read_pipeline/nodes/ScalerNode.h, C/C++, 29 lines
dorado/read_pipeline/nodes/include/read_pipeline/nodes/StereoDuplexEncoderNode.h, C/C++, 32 lines
dorado/read_pipeline/nodes/include/read_pipeline/nodes/SubreadTaggerNode.h, C/C++, 54 lines
dorado/read_pipeline/nodes/include/read_pipeline/nodes/TrimmerNode.h, C/C++, 29 lines
dorado/read_pipeline/nodes/include/read_pipeline/nodes/WriterNode.h, C/C++, 37 lines
dorado/resume_loader/ResumeLoader.cpp, C++, 82 lines
dorado/resume_loader/include/resume_loader/ResumeLoader.h, C/C++, 24 lines
dorado/secondary/architectures/flash_attention3_backend.cpp, C++, 209 lines
dorado/secondary/architectures/flash_attention3_backend.h, C/C++, 59 lines
dorado/secondary/architectures/flash_attention_module.cpp, C++, 325 lines
dorado/secondary/architectures/flash_attention_module.h, C/C++, 66 lines
dorado/secondary/architectures/include/secondary/architectures/model_config.h, C/C++, 37 lines
dorado/secondary/architectures/include/secondary/architectures/model_config_validation.h, C/C++, 61 lines
dorado/secondary/architectures/include/secondary/architectures/model_factory.h, C/C++, 30 lines
dorado/secondary/architectures/include/secondary/architectures/model_herro.h, C/C++, 91 lines
dorado/secondary/architectures/include/secondary/architectures/model_torch_base.h, C/C++, 110 lines
dorado/secondary/architectures/include/secondary/architectures/model_weights.h, C/C++, 15 lines
dorado/secondary/architectures/model_config.cpp, C++, 183 lines
dorado/secondary/architectures/model_config_validation.cpp, C++, 495 lines
dorado/secondary/architectures/model_factory.cpp, C++, 173 lines
dorado/secondary/architectures/model_gru.cpp, C++, 53 lines
dorado/secondary/architectures/model_gru.h, C/C++, 36 lines
dorado/secondary/architectures/model_herro.cpp, C++, 180 lines
dorado/secondary/architectures/model_latent_space_lstm.cpp, C++, 310 lines
dorado/secondary/architectures/model_latent_space_lstm.h, C/C++, 108 lines
dorado/secondary/architectures/model_slot_attention_consensus.cpp, C++, 627 lines
dorado/secondary/architectures/model_slot_attention_consensus.h, C/C++, 132 lines
dorado/secondary/architectures/model_torch_base.cpp, C++, 83 lines
dorado/secondary/architectures/model_variant_perceiver.cpp, C++, 1,257 lines
dorado/secondary/architectures/model_variant_perceiver.h, C/C++, 383 lines
dorado/secondary/architectures/model_weights.cpp, C++, 145 lines
dorado/secondary/common/alignment.cpp, C++, 33 lines
dorado/secondary/common/bam_file.cpp, C++, 167 lines
dorado/secondary/common/bam_info.cpp, C++, 138 lines
dorado/secondary/common/batching.cpp, C++, 88 lines
dorado/secondary/common/include/secondary/common/alignment.h, C/C++, 44 lines
dorado/secondary/common/include/secondary/common/bam_file.h, C/C++, 72 lines
dorado/secondary/common/include/secondary/common/bam_info.h, C/C++, 29 lines
dorado/secondary/common/include/secondary/common/batched_data.h, C/C++, 18 lines
dorado/secondary/common/include/secondary/common/batching.h, C/C++, 72 lines
dorado/secondary/common/include/secondary/common/device_info.h, C/C++, 15 lines
dorado/secondary/common/include/secondary/common/interval.h, C/C++, 29 lines
dorado/secondary/common/include/secondary/common/interval_tree_types.h, C/C++, 14 lines
dorado/secondary/common/include/secondary/common/region.h, C/C++, 66 lines
dorado/secondary/common/include/secondary/common/stats.h, C/C++, 37 lines
dorado/secondary/common/include/secondary/common/variant.h, C/C++, 47 lines
dorado/secondary/common/include/secondary/common/vcf_writer.h, C/C++, 37 lines
dorado/secondary/common/include/secondary/common/window.h, C/C++, 27 lines
dorado/secondary/common/include/secondary/common/worker_return_status.h, C/C++, 12 lines
dorado/secondary/common/region.cpp, C++, 169 lines
dorado/secondary/common/variant.cpp, C++, 123 lines
dorado/secondary/common/vcf_writer.cpp, C++, 217 lines
dorado/secondary/common/window.cpp, C++, 28 lines
dorado/secondary/consensus/consensus_utils.cpp, C++, 198 lines
dorado/secondary/consensus/include/secondary/consensus/consensus_result.h, C/C++, 17 lines
dorado/secondary/consensus/include/secondary/consensus/consensus_utils.h, C/C++, 46 lines
dorado/secondary/consensus/include/secondary/consensus/sample.h, C/C++, 114 lines
dorado/secondary/consensus/include/secondary/consensus/sample_collate_utils.h, C/C++, 27 lines
dorado/secondary/consensus/include/secondary/consensus/sample_trimming.h, C/C++, 64 lines
dorado/secondary/consensus/include/secondary/consensus/variant_calling.h, C/C++, 105 lines
dorado/secondary/consensus/include/secondary/consensus/variant_calling_sample.h, C/C++, 80 lines
dorado/secondary/consensus/include/secondary/consensus/window_utils.h, C/C++, 36 lines
dorado/secondary/consensus/sample.cpp, C++, 691 lines
dorado/secondary/consensus/sample_collate_utils.cpp, C++, 77 lines
dorado/secondary/consensus/sample_trimming.cpp, C++, 521 lines
dorado/secondary/consensus/variant_calling.cpp, C++, 1,373 lines
dorado/secondary/consensus/variant_calling_sample.cpp, C++, 412 lines
dorado/secondary/consensus/window_utils.cpp, C++, 132 lines
dorado/secondary/features/decoder_base.cpp, C++, 159 lines
dorado/secondary/features/decoder_factory.cpp, C++, 12 lines
dorado/secondary/features/encoder_counts.cpp, C++, 389 lines
dorado/secondary/features/encoder_counts.h, C/C++, 74 lines
dorado/secondary/features/encoder_factory.cpp, C++, 131 lines
dorado/secondary/features/encoder_read_alignment.cpp, C++, 536 lines
dorado/secondary/features/encoder_read_alignment.h, C/C++, 103 lines
dorado/secondary/features/encoder_utils.cpp, C++, 285 lines
dorado/secondary/features/include/secondary/features/decoder_base.h, C/C++, 88 lines
dorado/secondary/features/include/secondary/features/decoder_factory.h, C/C++, 13 lines
dorado/secondary/features/include/secondary/features/encoder_base.h, C/C++, 122 lines
dorado/secondary/features/include/secondary/features/encoder_factory.h, C/C++, 42 lines
dorado/secondary/features/include/secondary/features/encoder_utils.h, C/C++, 54 lines
dorado/secondary/features/include/secondary/features/haplotag_source.h, C/C++, 28 lines
dorado/secondary/features/include/secondary/features/kadayashi_options.h, C/C++, 20 lines
dorado/secondary/features/include/secondary/features/kadayashi_utils.h, C/C++, 24 lines
dorado/secondary/features/include/secondary/features/medaka_read_matrix.h, C/C++, 114 lines
dorado/secondary/features/include/secondary/features/variant_candidate_source.h, C/C++, 25 lines
dorado/secondary/features/kadayashi_utils.cpp, C++, 227 lines
dorado/secondary/features/medaka_bamiter.cpp, C++, 92 lines
dorado/secondary/features/medaka_bamiter.h, C/C++, 31 lines
dorado/secondary/features/medaka_counts.cpp, C++, 340 lines
dorado/secondary/features/medaka_counts.h, C/C++, 115 lines
dorado/secondary/features/medaka_read_matrix.cpp, C++, 677 lines
dorado/smallvar/include/variant/decode_data.h, C/C++, 19 lines
dorado/smallvar/include/variant/inference_data.h, C/C++, 17 lines
dorado/smallvar/include/variant/variant_impl.h, C/C++, 317 lines
dorado/smallvar/include/variant/variant_resources.h, C/C++, 23 lines
dorado/smallvar/variant_impl.cpp, C++, 2,205 lines
dorado/splitter/DuplexReadSplitter.cpp, C++, 697 lines
dorado/splitter/RNAReadSplitter.cpp, C++, 136 lines
dorado/splitter/include/splitter/DuplexReadSplitter.h, C/C++, 42 lines
dorado/splitter/include/splitter/RNAReadSplitter.h, C/C++, 36 lines
dorado/splitter/include/splitter/ReadSplitter.h, C/C++, 109 lines
dorado/splitter/include/splitter/myers.h, C/C++, 20 lines
dorado/splitter/myers.cpp, C++, 170 lines
dorado/splitter/splitter_utils.cpp, C++, 318 lines
dorado/splitter/splitter_utils.h, C/C++, 47 lines
dorado/splitter/tests/test_splitter_utils.cpp, C++, 312 lines
dorado/torch_utils/cuda_utils.cpp, C++, 402 lines
dorado/torch_utils/duplex_utils.cpp, C++, 117 lines
dorado/torch_utils/gpu_monitor.cpp, C++, 798 lines
dorado/torch_utils/include/torch_utils/auto_detect_device.h, C/C++, 24 lines
dorado/torch_utils/include/torch_utils/cuda_utils.h, C/C++, 72 lines
dorado/torch_utils/include/torch_utils/duplex_utils.h, C/C++, 32 lines
dorado/torch_utils/include/torch_utils/gpu_monitor.h, C/C++, 77 lines
dorado/torch_utils/include/torch_utils/gpu_profiling.h, C/C++, 101 lines
dorado/torch_utils/include/torch_utils/metal_utils.h, C/C++, 131 lines
dorado/torch_utils/include/torch_utils/module_utils.h, C/C++, 35 lines
dorado/torch_utils/include/torch_utils/tensor_utils.h, C/C++, 68 lines
dorado/torch_utils/include/torch_utils/torch_utils.h, C/C++, 13 lines
dorado/torch_utils/include/torch_utils/trim.h, C/C++, 57 lines
dorado/torch_utils/metal_utils.cpp, C++, 456 lines
dorado/torch_utils/pch/main.cpp, C++, 2 lines
dorado/torch_utils/pch/precompiled.cpp, C++, 1 line
dorado/torch_utils/pch/precompiled.h, C/C++, 1 line
dorado/torch_utils/tensor_utils.cpp, C++, 339 lines
dorado/torch_utils/torch_utils.cpp, C++, 73 lines
dorado/torch_utils/trim.cpp, C++, 184 lines
dorado/utils/ResourceLimiter.cpp, C++, 97 lines
dorado/utils/SampleSheet.cpp, C++, 450 lines
dorado/utils/alignment_utils.cpp, C++, 52 lines
dorado/utils/barcode_kits.cpp, C++, 1,861 lines
dorado/utils/basecaller_utils.cpp, C++, 27 lines
dorado/utils/benchmark_timer.cpp, C++, 40 lines
dorado/utils/cigar.cpp, C++, 62 lines
dorado/utils/concurrency/AsyncExecutor.cpp, C++, 15 lines
dorado/utils/concurrency/TaskPool.cpp, C++, 102 lines
dorado/utils/concurrency/WorkerPool.cpp, C++, 144 lines
dorado/utils/concurrency/async_task_executor.cpp, C++, 86 lines
dorado/utils/concurrency/detail/priority_task_queue.cpp, C++, 86 lines
dorado/utils/concurrency/multi_queue_thread_pool.cpp, C++, 158 lines
dorado/utils/container_utils.cpp, C++, 44 lines
dorado/utils/crash_handlers.cpp, C++, 133 lines
dorado/utils/crypto_utils.cpp, C++, 24 lines
dorado/utils/dev_utils.cpp, C++, 28 lines
dorado/utils/fs_utils.cpp, C++, 155 lines
dorado/utils/include/utils/AsyncQueue.h, C/C++, 329 lines
dorado/utils/include/utils/FixedSizeQueue.h, C/C++, 102 lines
dorado/utils/include/utils/FunctionRef.h, C/C++, 89 lines
dorado/utils/include/utils/MoveOnlyFunction.h, C/C++, 210 lines
dorado/utils/include/utils/PostCondition.h, C/C++, 24 lines
dorado/utils/include/utils/ResourceLimiter.h, C/C++, 68 lines
dorado/utils/include/utils/SampleSheet.h, C/C++, 130 lines
dorado/utils/include/utils/SeparatedStream.h, C/C++, 86 lines
dorado/utils/include/utils/alignment_utils.h, C/C++, 30 lines
dorado/utils/include/utils/arg_parse_ext.h, C/C++, 61 lines
dorado/utils/include/utils/barcode_kits.h, C/C++, 66 lines
dorado/utils/include/utils/basecaller_utils.h, C/C++, 7 lines
dorado/utils/include/utils/benchmark_timer.h, C/C++, 27 lines
dorado/utils/include/utils/cigar.h, C/C++, 103 lines
dorado/utils/include/utils/concurrency/AsyncExecutor.h, C/C++, 49 lines
dorado/utils/include/utils/concurrency/Task.h, C/C++, 32 lines
dorado/utils/include/utils/concurrency/TaskPool.h, C/C++, 69 lines
dorado/utils/include/utils/concurrency/WorkerPool.h, C/C++, 54 lines
dorado/utils/include/utils/concurrency/async_task_executor.h, C/C++, 63 lines
dorado/utils/include/utils/concurrency/detail/priority_task_queue.h, C/C++, 72 lines
dorado/utils/include/utils/concurrency/multi_queue_thread_pool.h, C/C++, 89 lines
dorado/utils/include/utils/concurrency/synchronisation.h, C/C++, 153 lines
dorado/utils/include/utils/concurrency/task_priority.h, C/C++, 10 lines
dorado/utils/include/utils/container_utils.h, C/C++, 56 lines
dorado/utils/include/utils/context_container.h, C/C++, 123 lines
dorado/utils/include/utils/crash_handlers.h, C/C++, 16 lines
dorado/utils/include/utils/crypto_utils.h, C/C++, 11 lines
dorado/utils/include/utils/dev_utils.h, C/C++, 36 lines
dorado/utils/include/utils/fs_utils.h, C/C++, 50 lines
dorado/utils/include/utils/hardware_interference_size.h, C/C++, 35 lines
dorado/utils/include/utils/io_utils.h, C/C++, 17 lines
dorado/utils/include/utils/jthread.h, C/C++, 30 lines
dorado/utils/include/utils/locale_utils.h, C/C++, 7 lines
dorado/utils/include/utils/log_utils.h, C/C++, 48 lines
dorado/utils/include/utils/math_utils.h, C/C++, 102 lines
dorado/utils/include/utils/memory_utils.h, C/C++, 11 lines
dorado/utils/include/utils/overlap.h, C/C++, 15 lines
dorado/utils/include/utils/overloaded.h, C/C++, 25 lines
dorado/utils/include/utils/paf_utils.h, C/C++, 57 lines
dorado/utils/include/utils/parameters.h, C/C++, 40 lines
dorado/utils/include/utils/rle.h, C/C++, 38 lines
dorado/utils/include/utils/scoped_trace_log.h, C/C++, 21 lines
dorado/utils/include/utils/sequence_utils.h, C/C++, 162 lines
dorado/utils/include/utils/simd.h, C/C++, 73 lines
dorado/utils/include/utils/stats.h, C/C++, 103 lines
dorado/utils/include/utils/stream_utils.h, C/C++, 100 lines
dorado/utils/include/utils/string_utils.h, C/C++, 214 lines
dorado/utils/include/utils/sys_stats.h, C/C++, 14 lines
dorado/utils/include/utils/sys_utils.h, C/C++, 7 lines
dorado/utils/include/utils/thread_utils.h, C/C++, 15 lines
dorado/utils/include/utils/time_utils.h, C/C++, 27 lines
dorado/utils/include/utils/timer_high_res.h, C/C++, 46 lines
dorado/utils/include/utils/tty_utils.h, C/C++, 38 lines
dorado/utils/include/utils/types.h, C/C++, 139 lines
dorado/utils/include/utils/uuid_utils.h, C/C++, 26 lines
dorado/utils/io_utils.cpp, C++, 23 lines
dorado/utils/locale_utils.cpp, C++, 44 lines
dorado/utils/log_utils.cpp, C++, 110 lines
dorado/utils/memory_utils.cpp, C++, 119 lines
dorado/utils/paf_utils.cpp, C++, 86 lines
dorado/utils/parameters.cpp, C++, 43 lines
dorado/utils/scoped_trace_log.cpp, C++, 28 lines
dorado/utils/sequence_utils.cpp, C++, 508 lines
dorado/utils/stats.cpp, C++, 111 lines
dorado/utils/sys_stats.cpp, C++, 43 lines
dorado/utils/sys_utils.cpp, C++, 24 lines
dorado/utils/tests/test_AsyncExecutor.cpp, C++, 412 lines
dorado/utils/tests/test_FunctionRef.cpp, C++, 131 lines
dorado/utils/tests/test_MoveOnlyFunction.cpp, C++, 176 lines
dorado/utils/thread_utils.cpp, C++, 264 lines
dorado/utils/time_utils.cpp, C++, 108 lines
dorado/utils/uuid_utils.cpp, C++, 38 lines
regression_test/__init__.py, Python, 1 line
regression_test/benchmarking.py, Python, 199 lines
regression_test/data_paths.py, Python, 27 lines
regression_test/run_benchmarking_tests.py, Python, 340 lines
regression_test/test_compare_platforms.py, Python, 89 lines
regression_test/test_dorado.py, Python, 323 lines
regression_test/utilities.py, Python, 46 lines
tests/AdapterDetectorTest.cpp, C++, 677 lines
tests/AlignerTest.cpp, C++, 736 lines
tests/AsyncQueueTest.cpp, C++, 339 lines
tests/BamReaderTest.cpp, C++, 124 lines
tests/BamUtilsTest.cpp, C++, 255 lines
tests/BamWriterTest.cpp, C++, 165 lines
tests/BarcodeClassifierSelectorTest.cpp, C++, 62 lines
tests/BarcodeClassifierTest.cpp, C++, 553 lines
tests/BasecallModelConfigTest.cpp, C++, 424 lines
tests/BatchParamsTest.cpp, C++, 161 lines
tests/ChunkTest.cpp, C++, 288 lines
tests/CigarTest.cpp, C++, 207 lines
tests/CliUtilsTest.cpp, C++, 41 lines
tests/CorrectionWindowTest.cpp, C++, 275 lines
tests/CustomBarcodeParserTest.cpp, C++, 210 lines
tests/DuplexReadTaggingNodeTest.cpp, C++, 87 lines
tests/DuplexSplitTest.cpp, C++, 254 lines
tests/FastqTagsTest.cpp, C++, 320 lines
tests/FastxRandomReaderTest.cpp, C++, 100 lines
tests/FastxSequentialReaderTest.cpp, C++, 133 lines
tests/FileInfoTest.cpp, C++, 112 lines
tests/FixedSizeQueueTest.cpp, C++, 184 lines
tests/HeaderMapperTest.cpp, C++, 530 lines
tests/HtsFileTest.cpp, C++, 823 lines
tests/IndexFileAccessTest.cpp, C++, 280 lines
tests/KadayashiTest.cpp, C++, 1,635 lines
tests/MathUtilsTest.cpp, C++, 40 lines
tests/MergeHeadersTest.cpp, C++, 237 lines
tests/MessageSinkUtils.h, C/C++, 66 lines
tests/MetalLinearTest.cpp, C++, 199 lines
tests/Minimap2IndexTest.cpp, C++, 307 lines
tests/ModBaseChunkTest.cpp, C++, 308 lines
tests/ModBaseConfigTest.cpp, C++, 186 lines
tests/ModBaseContextTest.cpp, C++, 81 lines
tests/ModBaseEncoderTest.cpp, C++, 605 lines
tests/ModelComplexTest.cpp, C++, 487 lines
tests/ModelKitsTest.cpp, C++, 192 lines
tests/ModelMetadataTest.cpp, C++, 225 lines
tests/ModelUtilsTest.cpp, C++, 202 lines
tests/MotifMatcherTest.cpp, C++, 43 lines
tests/NodeSmokeTest.cpp, C++, 480 lines
tests/PafUtilsTest.cpp, C++, 98 lines
tests/PairingNodeTest.cpp, C++, 146 lines
tests/PipelineTest.cpp, C++, 228 lines
tests/Pod5DataLoaderTest.cpp, C++, 134 lines
tests/PolyACalculatorTest.cpp, C++, 242 lines
tests/PostConditionTest.cpp, C++, 43 lines
tests/RNASplitTest.cpp, C++, 45 lines
tests/ReadFilterNodeTest.cpp, C++, 160 lines
tests/ReadForwarderNodeTest.cpp, C++, 31 lines
tests/ReadTest.cpp, C++, 451 lines
tests/ReadToBamTypeNodeTest.cpp, C++, 33 lines
tests/RealignMovesTest.cpp, C++, 185 lines
tests/ResourceLimiterTest.cpp, C++, 318 lines
tests/ResumeLoaderTest.cpp, C++, 28 lines
tests/RleTest.cpp, C++, 90 lines
tests/SamUtilsTest.cpp, C++, 234 lines
tests/SampleSheetTests.cpp, C++, 208 lines
tests/ScaledDotProductAttention.cpp, C++, 60 lines
tests/SecondaryBamFileTest.cpp, C++, 208 lines
tests/SecondaryDecodeVariantsTest.cpp, C++, 821 lines
tests/SecondaryEncoderReadAlignmentTest.cpp, C++, 1,844 lines
tests/SecondaryEncoderUtilsTest.cpp, C++, 798 lines
tests/SecondaryKadayashiUtils.cpp, C++, 156 lines
tests/SecondaryMergeVCSamplesTest.cpp, C++, 211 lines
tests/SecondaryModelConfigValidation.cpp, C++, 556 lines
tests/SecondaryModelFactory.cpp, C++, 1,157 lines
tests/SecondaryModelVariantPerceiverTest.cpp, C++, 111 lines
tests/SecondaryNormalizeVariantsTest.cpp, C++, 428 lines
tests/SecondarySampleCollateUtilsTest.cpp, C++, 182 lines
tests/SecondarySampleTest.cpp, C++, 798 lines
tests/SecondaryTrimTest.cpp, C++, 635 lines
tests/SecondaryWindowTest.cpp, C++, 208 lines
tests/SeparatedStreamTest.cpp, C++, 170 lines
tests/SequenceUtilsTest.cpp, C++, 326 lines
tests/StereoDuplexTest.cpp, C++, 87 lines
tests/StitchTest.cpp, C++, 169 lines
tests/StringUtilsTest.cpp, C++, 226 lines
tests/SummaryFileWriterTest.cpp, C++, 79 lines
tests/TensorUtilsTest.cpp, C++, 198 lines
tests/TestUtils.cpp, C++, 96 lines
tests/TestUtils.h, C/C++, 55 lines
tests/TimeUtilsTest.cpp, C++, 89 lines
tests/TrimTest.cpp, C++, 408 lines
tests/VCFWriterTest.cpp, C++, 255 lines
tests/VariantImplTest.cpp, C++, 2,211 lines
tests/WriterNodeTest.cpp, C++, 247 lines
tests/arg_parse_ext_test.cpp, C++, 36 lines
tests/async_task_executor_test.cpp, C++, 209 lines
tests/bed_file_test.cpp, C++, 289 lines
tests/check_shell_tests_active.sh, Shell, 8 lines
tests/context_container_test.cpp, C++, 272 lines
tests/cram/cram_shell_wrapper.sh, Shell, 34 lines
tests/cram/variant/helpers.sh, Shell, 49 lines
tests/cuda_utils_test.cpp, C++, 84 lines
tests/data/variant/test-03-kadayashi-varcall/run-construct-varcall.sh, Shell, 22 lines
tests/gpu_monitor_test.cpp, C++, 359 lines
tests/main.cpp, C++, 33 lines
tests/multi_queue_thread_pool_test.cpp, C++, 176 lines
tests/myers_test.cpp, C++, 96 lines
tests/priority_task_queue_test.cpp, C++, 181 lines
tests/synchronisation_test.cpp, C++, 248 lines
tests/test_dorado_correct.sh, Shell, 155 lines
tests/test_dorado_correct_cram.sh, Shell, 62 lines
tests/test_dorado_polish.sh, Shell, 86 lines
tests/test_dorado_variant.sh, Shell, 80 lines
tests/test_expected_logging.sh, Shell, 54 lines
tests/test_model_download.py, Python, 179 lines
tests/test_model_resolution.sh, Shell, 332 lines
tests/test_nested_output_structure.sh, Shell, 385 lines
tests/test_simple_basecaller_execution.sh, Shell, 1,006 lines
tests/test_utils.sh, Shell, 27 lines
tests/validate_bam.py, Python, 65 lines
tests/validate_fastq.py, Python, 54 lines
tests/validate_json.py, Python, 41 lines
tests/validate_split_bam.sh, Shell, 102 lines
tetra/setup.py, Python, 23 lines
tetra/test/__init__.py, Python, 1 line
tetra/test/test_compare_platforms.py, Python, 54 lines
tetra/test/test_data_checker.py, Python, 319 lines
tetra/test/test_data_update.py, Python, 327 lines
tetra/test/test_regression_manager.py, Python, 142 lines
tetra/tetra/__init__.py, Python, 30 lines
tetra/tetra/compare_platforms.py, Python, 105 lines
tetra/tetra/data_checker.py, Python, 171 lines
tetra/tetra/data_frame_utils.py, Python, 60 lines
tetra/tetra/database.py, Python, 245 lines
tetra/tetra/error_display.py, Python, 140 lines
tetra/tetra/graph_perf_results.py, Python, 323 lines
tetra/tetra/output_validation.py, Python, 176 lines
tetra/tetra/reformat_files.py, Python, 67 lines
tetra/tetra/regression_context.py, Python, 47 lines
tetra/tetra/regression_manager.py, Python, 307 lines
tetra/tetra/sequence_utils.py, Python, 343 lines
tetra/tetra/test_error_display.py, Python, 80 lines
tetra/tetra/timestamped_context.py, Python, 100 lines
tetra/tetra/update_reference_data.py, Python, 306 lines
tetra/tetra/upload_perf_results.py, Python, 322 lines
tetra/tetra/utilities.py, Python, 53 lines
LICENCE.txt, License, 323 lines
README.md, Text, 212 lines

At the source: github.com/nanoporetech/dorado

nanoporetech/modkit

License: GPL-3.0

State: the link answers, verified on 27 September 2026

Evidence: files inventoried

Commit: 5cecc3fb3a9336068d9e3c68d5c08d678153dd2c, 12 June 2026

Languages: Rust (108), JavaScript (8), Shell (8), Python (3)

Size: 419 files, 127 scripts

Software Heritage: archived

Found in: the text

Holds: README, license file, tests, continuous integration, documentation

Not found: CITATION.cff, environment file

Tools: SAMtools (3 files), pysam (2 files), NumPy (1 file), pandas (1 file), PyTorch (1 file)

Availability: 1 check, the latest on 27 September 2026: the link answers

27 September 2026: the link answers

129 files

docs/book-a0b12cfe.js, JavaScript, 843 lines
docs/clipboard-1626706a.min.js, JavaScript, 7 lines
docs/elasticlunr-ef4e11c1.min.js, JavaScript, 10 lines
docs/highlight-abc7f01d.js, JavaScript, 54 lines
docs/mark-09e88c2c.min.js, JavaScript, 7 lines
docs/searcher-c2a407aa.js, JavaScript, 555 lines
docs/searchindex-b348220b.js, JavaScript, 1 line
docs/toc-869b6773.js, JavaScript, 446 lines
generate_advanced_usage.sh, Shell, 92 lines
mac_compile_modkit.sh, Shell, 1,168 lines
modkit-core/src/adjust.rs, Rust, 438 lines
modkit-core/src/bedmethyl_util/mod.rs, Rust, 221 lines
modkit-core/src/bedmethyl_util/subcommands.rs, Rust, 794 lines
modkit-core/src/command_utils.rs, Rust, 456 lines
modkit-core/src/dmr/bedmethyl.rs, Rust, 453 lines
modkit-core/src/dmr/beta_diff.rs, Rust, 332 lines
modkit-core/src/dmr/isoform/gtf_reader.rs, Rust, 93 lines
modkit-core/src/dmr/isoform/mod.rs, Rust, 2,597 lines
modkit-core/src/dmr/isoform/pair.rs, Rust, 358 lines
modkit-core/src/dmr/isoform/scoring.rs, Rust, 181 lines
modkit-core/src/dmr/isoform/vis.rs, Rust, 265 lines
modkit-core/src/dmr/llr_model.rs, Rust, 437 lines
modkit-core/src/dmr/mod.rs, Rust, 9 lines
modkit-core/src/dmr/pairwise.rs, Rust, 310 lines
modkit-core/src/dmr/single_site.rs, Rust, 1,347 lines
modkit-core/src/dmr/subcommands.rs, Rust, 1,940 lines
modkit-core/src/dmr/tabix.rs, Rust, 374 lines
modkit-core/src/dmr/util.rs, Rust, 646 lines
modkit-core/src/entropy/methylation_entropy.rs, Rust, 358 lines
modkit-core/src/entropy/mod.rs, Rust, 1,695 lines
modkit-core/src/entropy/subcommand.rs, Rust, 518 lines
modkit-core/src/entropy/writers.rs, Rust, 349 lines
modkit-core/src/errs.rs, Rust, 115 lines
modkit-core/src/extract/args.rs, Rust, 181 lines
modkit-core/src/extract/mod.rs, Rust, 4 lines
modkit-core/src/extract/subcommand.rs, Rust, 1,196 lines
modkit-core/src/extract/util.rs, Rust, 868 lines
modkit-core/src/extract/writer.rs, Rust, 452 lines
modkit-core/src/fasta.rs, Rust, 368 lines
modkit-core/src/filter_thresholds.rs, Rust, 23 lines
modkit-core/src/genome_positions.rs, Rust, 132 lines
modkit-core/src/hmm.rs, Rust, 424 lines
modkit-core/src/interval_chunks.rs, Rust, 700 lines
modkit-core/src/lib.rs, Rust, 62 lines
modkit-core/src/localise/mod.rs, Rust, 2 lines
modkit-core/src/localise/subcommand.rs, Rust, 310 lines
modkit-core/src/localise/util.rs, Rust, 235 lines
modkit-core/src/logging.rs, Rust, 111 lines
modkit-core/src/mod_bam.rs, Rust, 2,919 lines
modkit-core/src/mod_base_code.rs, Rust, 459 lines
modkit-core/src/modbam_util/check_tags.rs, Rust, 466 lines
modkit-core/src/modbam_util/mod.rs, Rust, 2 lines
modkit-core/src/modbam_util/subcommands.rs, Rust, 2,475 lines
modkit-core/src/monoid.rs, Rust, 374 lines
modkit-core/src/motifs/args.rs, Rust, 172 lines
modkit-core/src/motifs/iupac.rs, Rust, 892 lines
modkit-core/src/motifs/mod.rs, Rust, 3,651 lines
modkit-core/src/motifs/motif_bed.rs, Rust, 808 lines
modkit-core/src/motifs/subcommand.rs, Rust, 1,131 lines
modkit-core/src/motifs/util.rs, Rust, 80 lines
modkit-core/src/parsing_utils.rs, Rust, 53 lines
modkit-core/src/pileup/base_mods_adapter.rs, Rust, 956 lines
modkit-core/src/pileup/bedrmod.rs, Rust, 240 lines
modkit-core/src/pileup/duplex.rs, Rust, 344 lines
modkit-core/src/pileup/mod.rs, Rust, 204 lines
modkit-core/src/pileup/pileup_processor.rs, Rust, 2,509 lines
modkit-core/src/pileup/subcommand.rs, Rust, 2,377 lines
modkit-core/src/position_filter.rs, Rust, 374 lines
modkit-core/src/read_cache.rs, Rust, 539 lines
modkit-core/src/read_ids_to_base_mod_probs.rs, Rust, 1,375 lines
modkit-core/src/reads_sampler/mod.rs, Rust, 391 lines
modkit-core/src/reads_sampler/record_sampler.rs, Rust, 107 lines
modkit-core/src/reads_sampler/sampling_schedule.rs, Rust, 1,072 lines
modkit-core/src/record_processor.rs, Rust, 34 lines
modkit-core/src/repair_tags.rs, Rust, 394 lines
modkit-core/src/sample_probs/mod.rs, Rust, 1,761 lines
modkit-core/src/stats/mod.rs, Rust, 101 lines
modkit-core/src/stats/subcommand.rs, Rust, 218 lines
modkit-core/src/summarize.rs, Rust, 488 lines
modkit-core/src/tabix.rs, Rust, 210 lines
modkit-core/src/threshold_mod_caller.rs, Rust, 482 lines
modkit-core/src/thresholds.rs, Rust, 260 lines
modkit-core/src/util.rs, Rust, 1,518 lines
modkit-core/src/validate/mod.rs, Rust, 1 line
modkit-core/src/validate/subcommand.rs, Rust, 1,134 lines
modkit-core/src/writers.rs, Rust, 1,475 lines
modkit-logging/src/lib.rs, Rust, 111 lines
modkit/src/commands.rs, Rust, 148 lines
modkit/src/main.rs, Rust, 32 lines
modkit/tests/common/mod.rs, Rust, 246 lines
modkit/tests/test_adjust_mods.rs, Rust, 483 lines
modkit/tests/test_bedmethyl_util.rs, Rust, 198 lines
modkit/tests/test_call_mods.rs, Rust, 326 lines
modkit/tests/test_dmr.rs, Rust, 80 lines
modkit/tests/test_entropy.rs, Rust, 41 lines
modkit/tests/test_extract.rs, Rust, 614 lines
modkit/tests/test_find_motifs.rs, Rust, 13 lines
modkit/tests/test_localize.rs, Rust, 11 lines
modkit/tests/test_modbam_utils.rs, Rust, 39 lines
modkit/tests/test_open_chromatin.rs, Rust, 79 lines
modkit/tests/test_pileup.rs, Rust, 1,018 lines
modkit/tests/test_pileup_hemi.rs, Rust, 62 lines
modkit/tests/test_repair.rs, Rust, 89 lines
modkit/tests/test_shell_completions.rs, Rust, 18 lines
modkit/tests/test_summary.rs, Rust, 171 lines
modkit/tests/test_update_tags.rs, Rust, 36 lines
modkit/tests/test_validate.rs, Rust, 54 lines
ochm/src/batcher.rs, Rust, 40 lines
ochm/src/feature_loader.rs, Rust, 132 lines
ochm/src/features.rs, Rust, 681 lines
ochm/src/lib.rs, Rust, 8 lines
ochm/src/models.rs, Rust, 132 lines
ochm/src/prob_merger.rs, Rust, 192 lines
ochm/src/range_feeder.rs, Rust, 243 lines
ochm/src/subcommand.rs, Rust, 429 lines
ochm/src/util.rs, Rust, 60 lines
safe-record/src/lib.rs, Rust, 122 lines
tests/add_implicit_col.py, Python, 28 lines
tests/add_mn_tags_to_repair_records.py, Python, 33 lines
tests/check_extracts.sh, Shell, 39 lines
tests/check_extracts_flag.sh, Shell, 84 lines
tests/common/mod.rs, Rust, 245 lines
tests/make_crams.sh, Shell, 10 lines
tests/make_trimmed_reads.sh, Shell, 21 lines
tests/regress_tags.sh, Shell, 9 lines
tests/trim_reads.py, Python, 28 lines
tests/update_extract_test_data.sh, Shell, 69 lines
LICENCE.txt, License, 323 lines
README.md, Text, 186 lines

At the source: github.com/nanoporetech/modkit

Wasatch-Biolabs-Bfx/MethylSeqR

License: other

State: the link answers, verified on 27 September 2026

Evidence: files inventoried

Commit: 42977bd32dd7b4079565dd09f76daa2489c3ce9f, 29 December 2025

Languages: R (42)

Size: 94 files, 42 scripts

Software Heritage: not archived

Found in: the text

Holds: README, license file, environment (DESCRIPTION), tests, documentation, 2 notebooks

Not found: CITATION.cff, continuous integration

Tools: tidyverse (19 files), ggplot2 (6 files)

Availability: 1 check, the latest on 27 September 2026: the link answers

27 September 2026: the link answers

44 files

R/calc_ch3_diff.R, R, 404 lines
R/calc_ch3_samplecor.R, R, 218 lines
R/ch3helper_cleanup.R, R, 9 lines
R/ch3helper_closeDB.R, R, 29 lines
R/ch3helper_connectDB.R, R, 54 lines
R/ch3helper_onLoad.R, R, 7 lines
R/ch3helper_positions.R, R, 137 lines
R/ch3helper_print.R, R, 51 lines
R/ch3helper_purgeTables.R, R, 31 lines
R/classify_ch3_reads.R, R, 159 lines, 1 match
R/collapse_ch3_windows.R, R, 130 lines, 1 match
R/export_ch3_table.R, R, 58 lines
R/filter_ch3_table.R, R, 70 lines
R/get_ch3_cols.R, R, 34 lines
R/get_ch3_cpg_count.R, R, 73 lines
R/get_ch3_dbinfo.R, R, 82 lines
R/get_ch3_stats.R, R, 194 lines
R/get_ch3_table.R, R, 53 lines
R/get_ch3_tableinfo.R, R, 76 lines
R/make_ch3_archive.R, R, 80 lines
R/make_ch3_db.R, R, 309 lines
R/plot_ch3_cov.R, R, 145 lines
R/plot_ch3_diff.R, R, 88 lines
R/plot_ch3_diff_density.R, R, 87 lines
R/plot_ch3_modfrac.R, R, 149 lines
R/plot_ch3_pca.R, R, 147 lines
R/remove_ch3_table.R, R, 34 lines
R/rename_ch3_samples.R, R, 162 lines
R/run_ch3_analysis.R, R, 212 lines
R/run_ch3_dplyr.R, R, 124 lines
R/run_ch3_qc.R, R, 79 lines
R/summarize_ch3_positions.R, R, 218 lines
R/summarize_ch3_reads.R, R, 121 lines
R/summarize_ch3_regions.R, R, 293 lines
R/summarize_ch3_windows.R, R, 246 lines
R/trim_ch3_reads.R, R, 144 lines
R/zzz.R, R, 56 lines
doc/MethylSeqRWalkthrough.R, R, 197 lines
doc/MethylSeqRWalkthrough.Rmd, R, 510 lines
tests/testthat.R, R, 12 lines
tests/testthat/test-calc_ch3_diff.R, R, 199 lines
vignettes/MethylSeqRWalkthrough.Rmd, R, 510 lines
LICENSE, License, 162 lines
README.md, Text, 233 lines

At the source: github.com/Wasatch-Biolabs-Bfx/MethylSeqR

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

3 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
919 scripts, each with its path and the digest of its content;
4 matches between paragraphs of the paper and lines of the code (method lexical-v1);
neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

No dataset and no data link were found in the paper.

Data availability statement

The original contributions presented in the study are publicly available. This data can be found here: Data has been made available NCBI’s Sequence Read Archive (SRA) under the project name ‘Circulating neuron-derived cfDNA for blood-based detection of Alzheimer’s and other neurodegenerative conditions’ and under the BioProject ID PRJNA1503594.

Reproduced under the paper's license (CC BY), from the paper cited above.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 3, 28 September 2026

Funding: added Utah State University; Brigham Young University

Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, pages, dates, 8 authors, 8 keywords, 10 MeSH terms, 95 references.

Cite

This paper

Pollard, C., Miller, R., Stirland, I., Keni, M., Jenkins, A., Saito, E., Hill, J. T., & Jenkins, T. (2026). Circulating neuron-derived cfDNA for blood-based detection of Alzheimer's and other neurodegenerative conditions. Frontiers in neurology, 17, 1822479. https://doi.org/10.3389/fneur.2026.1822479

BibTeX

@article{pollard2026circulating, author = {Pollard, Chad and Miller, Ryan and Stirland, Isaac and Keni, Mykle and Jenkins, Andrew and Saito, Erin and Hill, Jonathon T and Jenkins, Tim}, title = {{Circulating neuron-derived cfDNA for blood-based detection of Alzheimer's and other neurodegenerative conditions}}, journal = {Frontiers in neurology}, year = {2026}, month = aug, volume = {17}, pages = {1822479}, publisher = {Frontiers Media SA}, issn = {1664-2295}, doi = {10.3389/fneur.2026.1822479}, url = {https://doi.org/10.3389/fneur.2026.1822479}, pmid = {42626456}, pmcid = {PMC13491437} }

RIS

TY - JOUR AU - Pollard, Chad AU - Miller, Ryan AU - Stirland, Isaac AU - Keni, Mykle AU - Jenkins, Andrew AU - Saito, Erin AU - Hill, Jonathon T AU - Jenkins, Tim TI - Circulating neuron-derived cfDNA for blood-based detection of Alzheimer's and other neurodegenerative conditions T2 - Frontiers in neurology J2 - Front Neurol PY - 2026 DA - 2026/08/06 VL - 17 SP - 1822479 SN - 1664-2295 PB - Frontiers Media SA DO - 10.3389/fneur.2026.1822479 UR - https://doi.org/10.3389/fneur.2026.1822479 LA - en ER -

CSL-JSON

{ "id": "10.3389/fneur.2026.1822479", "type": "article-journal", "title": "Circulating neuron-derived cfDNA for blood-based detection of Alzheimer's and other neurodegenerative conditions", "container-title": "Frontiers in neurology", "author": [ { "family": "Pollard", "given": "Chad" }, { "family": "Miller", "given": "Ryan" }, { "family": "Stirland", "given": "Isaac" }, { "family": "Keni", "given": "Mykle" }, { "family": "Jenkins", "given": "Andrew" }, { "family": "Saito", "given": "Erin" }, { "family": "Hill", "given": "Jonathon T" }, { "family": "Jenkins", "given": "Tim" } ], "container-title-short": "Front Neurol", "volume": "17", "page": "1822479", "DOI": "10.3389/fneur.2026.1822479", "PMID": "42626456", "PMCID": "PMC13491437", "ISSN": "1664-2295", "publisher": "Frontiers Media SA", "URL": "https://doi.org/10.3389/fneur.2026.1822479", "language": "en", "issued": { "date-parts": [ [ 2026, 8, 6 ] ] } }

The tracing map gets a citation of its own once an author has validated it and it has a DOI.

Contribute

The authors of this paper can claim it, correct its record and validate its tracing map, and the maintainers of its code (its owner, or a public member of its organization) correct what it says of their repository; anyone signed in can ask for its removal. Every request goes to OSCR's own machine, which answers it; your account page follows them.

Sign in with ORCID to claim this paper as one of its authors, correct its record or validate its tracing map: when the paper's metadata lists your ORCID iD, you are recognized at once. Maintainers of its code: sign in with GitHub, then claim the repository on your account page.

Request its removal

To ask OSCR to remove this record, the copies of its authors' scripts or its tracing map, use the removal request page: signed in, you say who you are, what to remove and why, then review and confirm the request. Published rules decide every request (how).

Discussion, reproductions, activity

Discussion: questions and error reports about this paper and its code, from signed-in readers and its authors. It opens with sign-in.

Reproductions: reports from readers who ran the authors' code: what they reproduced, with which environment, commit and data. It opens with sign-in.

Activity: what happens around this paper: new versions of its record, its map's validation, discussions and reproductions. It opens with sign-in.

Circulating neuron-derived cfDNA for blood-based detection of Alzheimer's and other neurodegenerative conditions.

Code ↔ Paper

Paper

The authors' code

Overview

Abstract

Repositories

nanoporetech/dorado

nanoporetech/modkit

Wasatch-Biolabs-Bfx/MethylSeqR

Tracing map

Data

Data availability statement

Versions

Version 3, 28 September 2026

Version 1, 27 September 2026: the first record

Cite

This paper

Similar papers

Contribute

Claim this paper

Correct its record

Validate its tracing map

Add the badge to its README

Request its removal

Discussion, reproductions, activity