Bio Assembly QC

Assemble isolate genomes or metagenomes from QC-passed reads, normalize the assembler output to one contigs.fasta per sample, and run QUAST or MetaQUAST.

Instructions

Tool guides and versions: docs/README.md.

1. Validate the assembly manifest and inspect a restartable execution plan before starting expensive work:

   uv run --script skills/bio-assembly-qc/scripts/run_assembly_qc.py \
     assemblies.tsv --out results/bio-assembly-qc --threads 4
   # Inspect run_manifest.json, then execute the same plan on a compute node:
   uv run --script skills/bio-assembly-qc/scripts/run_assembly_qc.py \
     assemblies.tsv --out results/bio-assembly-qc --threads 16 --execute

The driver rejects samples whose upstream read_qc_status is not passed. It runs SPAdes (--isolate), metaSPAdes, Flye/metaFlye, or metaMDBG by mode, passes --threads to every tool (default 4; SPAdes otherwise uses 16), normalizes the assembler output to per-sample contigs.fasta, and chooses QUAST or MetaQUAST from the mode. It reuses a stage only when its declared outputs are non-empty and its .done marker exists. Run --execute through the scheduler (sbatch) for anything beyond the fixtures, not on a login node.

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+ (v4.3.0 current). Use metaSPAdes for short-read metagenomes.
• Long-read bacterial isolates (PacBio CLR, ONT): Flye v2.9.5+ for the draft assembly. Use Autocycler v0.6+ when a complete bacterial consensus genome is needed from several independent long-read assemblies; do not use it for mixed communities.
• Long-read metagenomes: Flye v2.9.5+ in --meta mode (metaFlye) as the baseline for ONT and CLR communities.
• HiFi metagenomes: metaMDBG v1.1+. In its benchmark it recovered up to twice as many circularized high-quality MAGs as metaFlye on HiFi data (see docs/README.md). Keep metaFlye as a comparator when a per-sample failure is suspected.
• Very large or diverse long-read datasets where runtime limits the work: myloasm, when its read profile matches the dataset.
• The driver does not run Autocycler, hybrid SPAdes, or myloasm. Run those by hand and record the exact commands and versions.

1. Run assembly with resource-aware settings and record exact CLI, version, thread count, and RAM ceiling.

• For very large ONT/metagenome FASTQs, use /bio-reads-qc-mapping guidance for filtering and avoid redundant full-file raw-read preflights before filtering. Record raw file metadata (stat path, size, mtime), optionally run a small sampled check, and write seqkit stats after each produced read set.
• Use atomic output patterns for long-running filters and assemblies: write to .tmp, verify non-empty/readable output, then mv into the final path. Resume mode should skip existing final outputs only after sanity checks; when checks fail, use a tool-supported overwrite option or remove the corrupt final output before rerunning.
• For Flye/metaFlye failures or interrupted jobs, prefer --resume or --resume-from in the existing output directory when the prior run is structurally intact. Do not delete a large partial assembly unless logs or missing stage files show it is corrupted.

1. Summarize the QUAST v5.3+ or MetaQUAST report.tsv per sample (contig count, total length, N50, largest contig) against project thresholds.
2. 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.
3. 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.

Input Requirements

Prerequisites:

• Tools declared in the project's pinned Pixi environment. See docs/README.md for expected tools.
• Sufficient disk and RAM for chosen assembler.

Inputs:

• reads/.fastq.gz or reads/.fastq (raw or filtered reads; verify actual compression by content when suffixes are suspect).
• assemblies.tsv with sample_id, mode, read1, read2, read_qc_status, and read_platform; supported core modes are short_isolate, long_isolate, short_metagenome, long_metagenome, and hifi_metagenome. read_platform is required for long_isolate and long_metagenome, and selects the Flye error model: ont gives --nano-hq, pacbio-clr gives --pacbio-raw, pacbio-hifi gives --pacbio-hifi. Leave it empty for short-read modes; hifi_metagenome accepts only pacbio-hifi or an empty value.

Output

• results/bio-assembly-qc/run_manifest.json (validated rows, planned commands, and per-stage status after --execute)
• results/bio-assembly-qc/<sample_id>/assembler/ (raw assembler output)
• results/bio-assembly-qc/<sample_id>/contigs.fasta (normalized assembly)
• results/bio-assembly-qc/<sample_id>/quast/report.tsv (QUAST or MetaQUAST metrics)
• results/bio-assembly-qc/domain_routing.tsv (written by the /tracking-taxonomy-updates QuickClade step, not by the driver)
• stdout: the last line is one JSON envelope {ok, skill, out, manifest, warnings} (driver stdout contract in AGENTS.md)

Quality Gates

• [ ] Assembly size range and N50 distribution meet project thresholds.
• [ ] Every assembler output is normalized to a non-empty per-sample contigs.fasta before QC or downstream routing.
• [ ] On execution failure, preserve logs and report the failed command; retry only after diagnosing the cause and recording the changed parameters. Report unmet biological thresholds as results; never tune parameters solely to pass a gate.
• [ ] Verify reads are present and readable. If gzip -t fails on a .gz-named file, inspect magic bytes or file type before labeling it corrupt; it may be plain FASTQ with the wrong suffix.
• [ ] Check available disk space before assembly.
• [ ] For large ONT/metagenome inputs, raw file metadata and post-filter seqkit stats are recorded without redundant full-file raw preflight scans.
• [ ] Long-running filter outputs use .tmp plus atomic rename, and resume guards require a stage .done marker before reusing non-empty outputs.
• [ ] Flye/metaFlye logs are inspected before deciding whether to resume, rerun, or clean a partial output directory.
• [ ] 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

Use fixtures/assemblies.tsv as the executable short-read, long-read, and metagenome planning fixture.

Troubleshooting

Issue: Large ONT assembly workflow appears stalled before assembly Solution: Check whether the script is doing a raw full-file preflight (gzip -t, raw seqkit stats) instead of productive filtering. For urgent routing/assembly, replace raw full scans with metadata plus sampled checks, then run filtering and post-filter stats.

Issue: Flye job timed out or was interrupted Solution: Inspect flye.log and stage files. If the output directory is intact, resubmit with Flye resume options rather than restarting from scratch.