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bio-genome-assembly-assembly-polishing

Maintainer FreedomIntelligence · Last updated April 1, 2026

Polish assemblies with Medaka (ONT) or NextPolish (Illumina).

OpenClawNanoClawAnalysisReproductionbio-genome-assembly-assembly-polishing🧠 bioos extended suitebioos extended bioinformatics suitepolish

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

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

Maintainer
FreedomIntelligence
License
MIT
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

  • Improve assembly accuracy by correcting errors using additional sequencing data.
  • bwa index assembly.fasta bwa mem -t 16 assembly.fasta R1.fq.gz R2.fq.gz | samtools sort -o aligned.bam samtools index aligned.bam.

Source Doc

Excerpt From SKILL.md

Polishing Strategies

ToolInput ReadsBest For
PilonIlluminaFinal polishing
medakaONTONT assemblies
RaconLong readsQuick polishing
NextPolishBothCombined approach

ONT Assembly

  1. Racon (2-3 rounds with ONT)
  2. medaka (1 round)
  3. Pilon (2-3 rounds with Illumina)

PacBio CLR Assembly

  1. Racon (2-3 rounds)
  2. Pilon (2-3 rounds with Illumina)

Use cases

  • Use bio-genome-assembly-assembly-polishing for genomics and bioinformatics workflows.
  • Apply bio-genome-assembly-assembly-polishing 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

  • long-read-assembly - Initial assembly
  • short-read-assembly - Source of polishing reads
  • assembly-qc - Assess polishing improvement
  • long-read-sequencing - medaka variant calling

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