Bio Reads QC Mapping

When to use

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

Prerequisites

• Tools installed via pixi (see pixi.toml).
• Sample sheet and reads are available.

Inputs

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

Outputs

• 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/

Steps

1. Parse sample sheet and validate inputs.
2. For short reads: Run QC/trimming (bbduk).
3. For long reads: Trim adapters (Porechop) and filter by quality/length (Filtlong).
4. Map reads (bbmap or minimap2) and generate coverage tables.

QC 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.

Validation

• Validate sample sheet schema and FASTQ integrity.

Tools

• bbtools (bbduk, bbmap) v39.52
• minimap2 v2.30
• Filtlong (long read quality filtering)
• Porechop (Nanopore adapter trimming)

Paper summaries (2023-2025)

• summaries/ (include example use cases and tool settings used)

Tool documentation

• BBDuk - Quality trimming and adapter removal for short reads
• BBMap - Short read aligner and coverage calculator
• Minimap2 - Long read aligner
• Filtlong - Long read quality filtering
• Porechop - Nanopore adapter trimming

References

• See ../bio-skills-references.md