Validates FASTQ inputs and runs FastQC, MultiQC, fastp, and Cutadapt QC workflows.
npx skills add https://github.com/openai/plugins --skill ngs-fastq-qc
Please help me install this Agent Skill. Skill: ngs-fastq-qc Source: https://github.com/openai/plugins/tree/main/plugins/ngs-analysis/skills/ngs-fastq-qc Command: npx skills add https://github.com/openai/plugins --skill ngs-fastq-qc
Raw sequencing reads often contain adapter contamination, quality drops, pairing errors, or artifacts that silently corrupt downstream analysis. This Skill validates FASTQ inputs, runs standardized QC with FastQC and MultiQC, interprets the results, and only recommends trimming with fastp or Cutadapt when the evidence warrants it.
Ask the assistant to inspect your FASTQ files, infer R1/R2 pairings, run FastQC and MultiQC QC, and recommend whether trimming is needed.
High-intent search queries and answers about installing and using this skill.
Run FastQC on all FASTQ files with multithreading, then aggregate results with MultiQC into a single project report. This Skill automates both steps through its local runner, which also validates sample sheets and read pairing before execution.
Use Cutadapt when explicit adapter or primer sequences must be specified, and fastp when automatic all-in-one QC and trimming is acceptable. The Skill inspects QC signals first and recommends the appropriate branch rather than trimming by default.
No. The workflow never overwrites input FASTQs and preserves raw QC reports even when trimmed FASTQs are produced. Outputs go to a timestamped run directory containing manifests, logs, and reports.
High duplication can be expected for amplicons, targeted panels, or low-input libraries, while overrepresented sequences may be adapters, primers, rRNA, PhiX, or true biology. The Skill classifies these signals before recommending any filtering.
Avoid trimming when QC looks normal or when downstream analysis requires original read lengths, UMIs, or inline barcodes. The Skill inspects raw QC first and recommends a no-trimming path with rationale when warranted.
pradyumnasagarProcess paired-end FASTQ files with synchronized R1 and R2 reads.
pradyumnasagarAlign NGS short reads against a reference DNA genome using BWA-MEM.
TianGzlabPerform quality control on genomic sequencing data with FastQC and fastp.
jaechang-hitsTrim adapters and filter quality in FASTQ files using fastp.
