bio-reads-qc-mapping
Ingest, QC, and map reads with reproducible outputs. Use for raw read processing and coverage stats.
npx skills add BioTender-max/awesome-bio-agent-skills --skill bio-reads-qc-mapping --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# 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: trim adapters with `Porechop_ABI` (preferred; the original `Porechop` is unmaintained and ships stale adapter sets) or `Pychopper` for full-length cDNA. Filter by quality and length with `filtlong` v0.2.1. 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 require
- Instructions
- Quick Reference
- Input Requirements
- Output
- Quality Gates
- Examples
- Example 1: Expected input layout
- Troubleshooting
What does the bio-reads-qc-mapping skill do?
Ingest, QC, and map reads with reproducible outputs. Use for raw read processing and coverage stats.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill bio-reads-qc-mapping --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.