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FastaGuard v0.1.0

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@github-actions github-actions released this 18 May 18:01
· 139 commits to main since this release
v0.1.0
09d8ae3

FastaGuard v0.1.0

FastaGuard v0.1.0 is the first assembly-focused FASTA preflight release.

The promise is deliberately narrow:

Before QUAST. Before BUSCO. Before BlobToolKit. Before annotation.
Run FastaGuard first.

Highlights

  • Validates plain and gzipped assembly FASTA files.
  • Detects malformed or empty records, duplicate IDs, duplicate sequences, invalid symbols, high-N content, tiny contigs, and long N gap runs.
  • Reports N50, N90, L50, L90, GC%, AT%, N%, ambiguity rate, and core length statistics.
  • Adds machine-readable JSON Schema, finding catalog, structured actions, bounded per-record evidence, provenance, and scope limits.
  • Adds self-contained HTML reports with finding evidence, suggested actions, length histogram, and GC-vs-length plot.
  • Emits JSON, TSV, HTML, and MultiQC custom-content JSON.
  • Includes starter Nextflow, nf-core local module, and Snakemake examples.

Install From Release Assets

Download the archive for your platform, unpack it, and place fastaguard on PATH:

tar -xzf fastaguard-v0.1.0-x86_64-unknown-linux-gnu.tar.gz
./fastaguard-v0.1.0-x86_64-unknown-linux-gnu/fastaguard --help

macOS Intel and Apple Silicon archives are also built by the release workflow.

Docker

docker build -t fastaguard:local .
docker run --rm -v "$PWD:/data" fastaguard:local /data/sample.fa \
  --profile assembly \
  --out /data/fastaguard_report.html \
  --json /data/fastaguard.json \
  --tsv /data/fastaguard.tsv \
  --multiqc /data/fastaguard_mqc.json

Example Command

fastaguard sample.fa \
  --profile assembly \
  --out fastaguard_report.html \
  --json fastaguard.json \
  --tsv fastaguard.tsv \
  --multiqc fastaguard_mqc.json

Exit Codes

0 = pass
1 = warnings above configured threshold
2 = hard QC failure
3 = invalid input / tool error

Known Limits

  • v0.1.0 supports the assembly profile only.
  • FastaGuard does not estimate biological completeness, taxonomic contamination, or assembly correctness.
  • Use QUAST, BUSCO, BlobToolKit, CheckM, and related tools after FASTA preflight depending on the biological question.
  • Windows binaries, Bioconda, Homebrew, upstream nf-core submission, and official Snakemake wrapper submission are planned later.
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