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bio-workflows-longread-sv-pipeline

Maintainer FreedomIntelligence · Last updated April 1, 2026

Long-read structural variant calling and annotation pipeline.

OpenClawNanoClawAnalysisReproductionbio-workflows-longread-sv-pipeline🧠 bioos extended suitebioos extended bioinformatics suitelong

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

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

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

Complete workflow for detecting structural variants from ONT or PacBio long-read data.
NanoPlot --fastq reads.fastq.gz \ --outdir nanoplot_output \ --threads 8.

Source Doc

Excerpt From SKILL.md

ONT reads

minimap2 -ax map-ont
-t 16
--MD
-Y
reference.fa
reads.fastq.gz |
samtools sort -@ 4 -o aligned.bam

samtools index aligned.bam

PacBio HiFi

minimap2 -ax map-hifi
-t 16
--MD
-Y
reference.fa
reads.fastq.gz |
samtools sort -@ 4 -o aligned.bam

PacBio CLR

minimap2 -ax map-pb
-t 16
--MD
-Y
reference.fa
reads.fastq.gz |
samtools sort -@ 4 -o aligned.bam bash samtools flagstat aligned.bam samtools depth -a aligned.bam | awk '{sum+=$3} END {print "Average coverage:",sum/NR}'

- Mapping rate >90%
- Average coverage >10x for SV calling (>20x preferred)

Use cases

Use bio-workflows-longread-sv-pipeline for genomics and bioinformatics workflows.
Apply bio-workflows-longread-sv-pipeline to sequencing, variant, or omics analysis tasks.