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bio-genome-assembly-scaffolding

Maintainer FreedomIntelligence · Last updated April 1, 2026

Scaffold contigs with Hi-C, optical mapping, or long reads.

OpenClawNanoClawAnalysisReproductionbio-genome-assembly-scaffolding🧠 bioos extended suitebioos extended bioinformatics suitescaffold

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-genome-assembly-scaffolding

Maintainer
FreedomIntelligence
License
MIT
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

  • bwa index draft_assembly.fa bwa mem -5SP -t 16 draft_assembly.fa hic_R1.fq.gz hic_R2.fq.gz | \ samtools view -@ 8 -bhS - > aligned.bam.

Source Doc

Excerpt From SKILL.md

Convert BAM to BED

bedtools bamtobed -i aligned.bam | sort -k4 > aligned.bed

Run YaHS

yahs draft_assembly.fa aligned.bed -o scaffolds

Run with error correction

yahs draft_assembly.fa aligned.bed -o scaffolds --no-contig-ec

Use cases

  • Use bio-genome-assembly-scaffolding for genomics and bioinformatics workflows.
  • Apply bio-genome-assembly-scaffolding to sequencing, variant, or omics analysis tasks.

Not for

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

Upstream Related Skills

  • genome-assembly/long-read-assembly - Generate initial contigs
  • genome-assembly/assembly-polishing - Polish before scaffolding
  • genome-assembly/assembly-qc - Validate final assembly
  • hi-c-analysis/hic-data-io - Hi-C data processing

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