bio-reads-qc-mappinglisted

# 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. 5. Record the tool, version, and any GPU device used in the run log. ## 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 Q