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Bio Assembly QC
bio-assembly-qc
Assemble genomes/metagenomes and produce assembly QC artifacts.
SKILL.md
Full skill instructions
Bio Assembly QC
When to use
- Assemble genomes/metagenomes and produce assembly QC artifacts.
Prerequisites
- Tools installed via pixi (see pixi.toml).
- Sufficient disk and RAM for chosen assembler.
Inputs
- reads/*.fastq.gz (raw reads).
- assembler choice (spades | flye).
Outputs
- 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/
Steps
- Select assembler based on read type and genome size.
- Run assembly with resource-aware settings.
- Run QUAST/MetaQUAST and summarize metrics.
QC 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.
Validation
- Verify reads are present and gzip-readable.
- Check available disk space before assembly.
Tools
- spades v4.2.0
- flye v2.9.6
- quast v5.3.0
Paper summaries (2023-2025)
- summaries/ (include example use cases and tool settings used)
Tool documentation
- SPAdes - De novo genome/metagenome assembler
- Flye - Long-read assembly for PacBio and Nanopore
- QUAST - Assembly quality assessment and metrics
References
- See ../bio-skills-references.md
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