Individual skill
tooluniverse-fastq-qc
FASTQ quality control and adapter/quality-trimming decisions with local NGS tools — run FastQC on raw reads, summarize a project with MultiQC, interpret per-base sequence quality, per-base N content, adapter content, overrepresented sequences, sequence duplication and GC content, and decide whether (and how) to trim with fastp / Cutadapt before downstream analysis. seqkit for read counts/stats/subsampling. Use when someone asks "run QC on my FASTQs", "are my reads good quality?", "do I need to trim adapters?", "interpret this FastQC report", "what does this WARN/FAIL mean", "why are overrepresented sequences flagged", "should I quality-trim before alignment", "make a MultiQC summary", or "clean up these reads with fastp". NOT for differential expression / DEG analysis (use tooluniverse-rnaseq-deseq2), NOT for read alignment, coverage, or variant calling (use tooluniverse-variant-analysis / tooluniverse-sequence-analysis). Honest: shells out to real local binaries; if a tool is missing...
plugins/tooluniverse/skills/tooluniverse-fastq-qc/SKILL.md
Source commit 5598a9fc97e32964fe9b703818e7d0747142f179
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- Last checked
- Nov 9, 2026
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- Repository last updated
- Nov 8, 2026
- License
- Apache-2.0
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SKILL.mdcore · 11,865 bytesSKILL.mdcore · 11,865 bytesSKILL.mdcore · 11,865 bytesSKILL.mdcore · 11,865 bytesreferences/fastqc_interpretation.mddoc · 5,426 bytesreferences/tools_and_install.mddoc · 3,402 bytesreferences/trimming_decisions.mddoc · 2,769 bytesscripts/run_fastq_qc.pyruns · 9,751 bytes
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# FASTQ Quality Control & Trimming Decisions
Run quality control on raw sequencing reads, interpret the report, and make
an evidence-based decision about whether to trim — using real local
command-line tools (FastQC, MultiQC, fastp, Cutadapt, seqkit).
## Honesty contract (read first)
This skill drives **real binaries**. It must never fabricate QC numbers.
1. **Preflight before anything.** Check whether the required tools are on
PATH. If a required tool is missing, emit the install plan and STOP.
Do not estimate, guess, or describe hypothetical QC results.
2. **Never auto-trim.** Trimming is a *decision*. QC-only is the default.