Bio Assembly QC
Assemble genomes/metagenomes and produce assembly QC artifacts.
Instructions
- Select assembler based on read type and genome size.
- Run assembly with resource-aware settings.
- Run QUAST/MetaQUAST and summarize metrics.
Quick Reference
| 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 |
Input Requirements
Prerequisites:
- Tools available in the active environment (Pixi/conda/system). See
docs/README.mdfor expected tools. - Sufficient disk and RAM for chosen assembler. Inputs:
- reads/*.fastq.gz (raw reads).
- assembler choice (spades | flye).
Output
- results/bio-assembly-qc/contigs.fasta
- results/bio-assembly-qc/assembly_metrics.tsv
- results/bio-assembly-qc/qc_report.html
- results/bio-assembly-qc/logs/
Quality Gates
- Assembly size range and N50 distribution meet project thresholds.
- On failure: retry with alternative parameters; if still failing, record in report and exit non-zero.
- Verify reads are present and gzip-readable.
- Check available disk space before assembly.
Examples
Example 1: Expected input layout
reads/*.fastq.gz (raw reads).
assembler choice (spades | flye).
Troubleshooting
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.