Bio Assembly QC

Assemble genomes/metagenomes and produce assembly QC artifacts.

Instructions

1. Select assembler based on read type and genome size.
2. Run assembly with resource-aware settings.
3. 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.md for 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.