bio-assembly-qc

Bio Assembly QC

Assemble genomes/metagenomes and produce assembly QC artifacts.

Instructions

1. Select an assembler based on read type, genome/metagenome scope, and sample diversity:
   • Illumina short-read isolates and hybrid assemblies: SPAdes v4.0.0+ (final feature release; bug-fix-only series continues). Use metaSPAdes for short-read metagenomes.
   • Long-read bacterial isolates (PacBio CLR, ONT): Flye v2.9.5+ for the draft/baseline assembly. Use Autocycler v0.6+ when a complete, high-confidence bacterial consensus genome is needed from multiple independent long-read assembly attempts; do not use it for mixed-community metagenomes.
   • Long-read metagenomes: Flye v2.9.5+ in --meta mode (metaFlye) as the baseline for ONT/CLR mixed-community assemblies.
   • HiFi metagenomes: prefer metaMDBG v1.1 (~2× more circularized high-quality MAGs vs metaFlye on HiFi, better virus/plasmid recovery; Nature Biotechnology 2024, DOI: 10.1038/s41587-023-01983-6). Keep metaFlye as a comparator when a per-sample failure mode is suspected.
   • Diverse or very large long-read datasets where speed dominates: myloasm (2025) as a faster long-read metagenome assembler when its profile matches the dataset; document the choice in the run log.
2. Run assembly with resource-aware settings and record exact CLI, version, thread count, and RAM ceiling.
3. Run QUAST v5.3+ (use MetaQUAST for metagenomes) and summarize metrics.
4. For every produced contigs.fasta, invoke /tracking-taxonomy-updates to run the BBTools-container QuickClade percontig domain screen before choosing downstream genome/MAG/viral/eukaryotic workflows.
5. Use the QuickClade domain routing table to decide the next step:
   • Bacteria/Archaea -> /bio-gene-calling, /bio-annotation, and GTDB-Tk taxonomy assignment.
   • Viral or virus-like -> /bio-viromics before prokaryotic MAG tooling.
   • Eukaryota -> eukaryote-aware gene/QC workflows and EukCC where bins or genomes are present.
   • Mixed/low-confidence -> split or flag contigs before domain-specific analysis.

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.

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 | metaflye | metamdbg | myloasm | autocycler).

Output

• results/bio-assembly-qc/contigs.fasta
• results/bio-assembly-qc/assembly_metrics.tsv
• results/bio-assembly-qc/domain_routing.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.
• For Autocycler isolate consensus, record each input assembler/run and confirm the sample is not a mixed community.
• QuickClade percontig domain screen completed or the reason for skipping it is explicitly recorded.
• Domain routing table is reviewed before selecting MAG, viral, bacterial/archaeal, or eukaryotic downstream tools.

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.