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BI

bio-longread-qc

Maintainer FreedomIntelligence · Last updated April 1, 2026

Quality control for long-read sequencing data using NanoPlot, NanoStat, and chopper. Generate QC reports, filter reads by length and quality, and visualize read characteristics. Use when assessing ONT or PacBio run quality or filtering reads before assembly or alignment.

OpenClawNanoClawAnalysisWritingbio-longread-qc🧬 bioinformatics (gptomics bio-* suite)bioinformatics — sequencing & read qcquality

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-longread-qc

Maintainer
FreedomIntelligence
License
MIT
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

  • CLI: NanoPlot --fastq reads.fq.gz -o nanoplot_output/, chopper -q 10 -l 1000 < reads.fq > filtered.fq.
  • Check the quality of my Nanopore/PacBio run" → Generate read length distributions, quality score plots, and summary statistics, then filter reads by length and quality thresholds. CLI: NanoPlot --fastq reads.fq.gz -o nanoplot_output/, chopper -q 10 -l 1000 < reads.fq > filtered.fq.
  • NanoPlot --fastq reads.fastq.gz -o nanoplot_output -t 4.

Source Doc

Excerpt From SKILL.md

From BAM

NanoPlot --bam aligned.bam -o nanoplot_output -t 4

From sequencing summary (fastest)

NanoPlot --summary sequencing_summary.txt -o nanoplot_output


## Quick statistics (no plots)

NanoStat --fastq reads.fastq.gz --threads 4

Use cases

  • Use when assessing ONT or PacBio run quality or filtering reads before assembly or alignment.

Not for

  • Do not rely on this catalog entry alone for installation or maintenance details.

Upstream Related Skills

  • long-read-alignment - Align filtered reads
  • sequence-io/fastq-quality - FASTQ quality analysis
  • medaka-polishing - Polish with filtered reads

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