Bio Reads QC Mapping

Ingest, QC, and map reads with reproducible outputs. Use for raw read processing and coverage stats.

Instructions

1. Parse sample sheet and validate inputs.
2. For short reads: run QC and adapter/quality trimming with bbduk or fastp v1.3.3+.
3. For long reads: use current basecaller-aware QC first. For ONT, prefer Dorado summaries/trimming during basecalling or demultiplexing when starting from signal/BAM; for FASTQ-only filtering use chopper for quality/length/end trimming or filtlong v0.2.1 when selecting reads for assembly. Use Pychopper for full-length cDNA. Treat Porechop_ABI as a targeted legacy/fallback adapter-discovery tool, and record why it is needed.
4. Map reads and produce coverage tables:

• Short reads, CPU: bbmap or bwa-mem2 v2.2.1+. Short reads, GPU node available: NVIDIA Parabricks fq2bam (wraps bwa-mem2 + GATK markdup; typically 3–4× faster than bwa-mem2 on 8 cores and up to ~80× over a 96-core CPU pipeline).
• Long reads, CPU: minimap2 v2.30+. AVX-512 hardware: mm2-fast as a drop-in replacement (~1.8× speedup). GPU node available: mm2-gb or mm2-ax for CUDA-accelerated long-read alignment.

1. Record the tool, version, and any GPU device used in the run log.

Quick Reference

Input Requirements

Prerequisites:

• Tools available in the active environment (Pixi/conda/system). See docs/README.md for expected tools.
• Sample sheet and reads are available.

Inputs:

• sample_sheet.tsv
• reads/*.fastq.gz
• reference.fasta (optional)

Output

• results/bio-reads-qc-mapping/trimmed_reads/
• results/bio-reads-qc-mapping/qc_reports/
• results/bio-reads-qc-mapping/mapping_stats.tsv
• results/bio-reads-qc-mapping/coverage.tsv
• results/bio-reads-qc-mapping/logs/

Quality Gates

• [ ] Post-QC read count sanity checks pass.
• [ ] Mapping rate meets project thresholds.
• [ ] On failure: retry with alternative parameters; if still failing, record in report and exit non-zero.
• [ ] Validate sample sheet schema and FASTQ integrity.
• [ ] For long-read QC, record whether trimming happened in the basecaller/demultiplexer, chopper, filtlong, Pychopper, or a documented Porechop_ABI fallback.

Examples

Example 1: Expected input layout

sample_sheet.tsv
reads/*.fastq.gz
reference.fasta (optional)

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.