majiayu000 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
- Parse sample sheet and validate inputs.
- For short reads: Run QC/trimming (bbduk).
- For long reads: Trim adapters (Porechop) and filter by quality/length (Filtlong).
- 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