@deckyard/ngs

Streaming NGS file formats, read QC, interval arithmetic and pipeline orchestration

bioinformatics ngs sequencing fastq genomics

Depend on it

[decks]
"@deckyard/ngs" = "^0.2.0"

Versions

Version	Status	Kind	Pin	Requires	Engines	Capabilities
0.2.0	live	git	`fbdf26626612`	-	`jennifer >=0.25.0`	`exec`

License

LGPL-3.0-only

Source

Source: github.com/deckyard/deck-ngs
Released from: 0.2.0
Published under: @deckyard mplx
Repository owner: deckyard

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Readme

deck-ngs - `@deckyard/ngs`

Streaming FASTQ, SAM, VCF, BED and GFF3/GTF I/O, read QC, trimming, interval arithmetic and pipeline orchestration for next-generation sequencing data, in Jennifer. Memory use does not grow with file size. Alignment, assembly, variant calling and BAM/CRAM stay with the native tools, which the pipeline module drives.

Install

# deck.yaml
decks:
  "@deckyard/ngs": "^0.1.0"

jvc vendors the deck's src/ into vendor/deckyard/ngs/. Release archives are named deckyard-ngs-<version>.tar.gz; installing one by hand is covered in the manual.

Needs Jennifer 0.25.0 or newer. Streaming gzip and pipeline need the exec capability (the default jennifer binary, not jennifer-tiny) and gzip and mkfifo on PATH; everything else runs on both binaries.

Example

use io;
import "@deckyard/ngs/qc.j" as qc;

def report as qc.Report init qc.analyze("sample.fastq.gz", qc.options());
io.printf("%s", qc.summary($report));

Documentation

The manual is at https://deckyard.github.io/deck-ngs/, built from docs/. The cheatsheet lists every export.

Licence

This deck as JSON