bio-reads-qc-mapping

Original：🇺🇸 English

Translated

Ingest, QC, and map reads with reproducible outputs. Use for raw read processing and coverage stats.

1installs

Added on2026-02-21

NPX Install

npx skill4agent add fmschulz/omics-skills bio-reads-qc-mapping

Ingest, QC, and map reads with reproducible outputs. Use for raw read processing and coverage stats.

Parse sample sheet and validate inputs.
For short reads: Run QC/trimming (bbduk).
For long reads: Trim adapters (Porechop) and filter by quality/length (Filtlong).
Map reads (bbmap or minimap2) and generate coverage tables.

Task	Action
Run workflow	Follow the steps in this skill and capture outputs.
Validate inputs	Confirm required inputs and reference data exist.
Review outputs	Inspect reports and QC gates before proceeding.
Tool docs	See `docs/README.md` .
References	- See ../bio-skills-references.md

Prerequisites:

Tools available in the active environment (Pixi/conda/system). See
```
docs/README.md
```
for expected tools.
Sample sheet and reads are available. Inputs:
sample_sheet.tsv
reads/*.fastq.gz
reference.fasta (optional)

Post-QC read count sanity checks pass.
Mapping rate meets project thresholds.
On failure: retry with alternative parameters; if still failing, record in report and exit non-zero.
Validate sample sheet schema and FASTQ integrity.

text

sample_sheet.tsv
reads/*.fastq.gz
reference.fasta (optional)

Issue: Missing inputs or reference databases Solution: Verify paths and permissions before running the workflow.

Issue: Low-quality results or failed QC gates Solution: Review reports, adjust parameters, and re-run the affected step.