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.
# 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.
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));
The manual is at https://deckyard.github.io/deck-ngs/, built from docs/. The
cheatsheet lists every
export.
LGPL-3.0-only, see LICENSE. Copyright (C) 2026 mplx <mplx@jennifer-lang.dev>.