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bio-workflows-genome-assembly-pipeline

Maintainer FreedomIntelligence · Last updated April 1, 2026

De novo genome assembly: raw reads → assembly → QC → annotation.

OpenClawNanoClawAnalysisReproductionbio-workflows-genome-assembly-pipeline🧠 bioos extended suitebioos extended bioinformatics suitede

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

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

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

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

Complete workflow from sequencing reads to polished, quality-assessed genome assembly.
spades.py \ -1 trimmed_R1.fq.gz \ -2 trimmed_R2.fq.gz \ -o spades_output \ --careful \ -t 16 \ -m 64.

Source Doc

Excerpt From SKILL.md

For isolate genomes

spades.py --isolate
-1 trimmed_R1.fq.gz
-2 trimmed_R2.fq.gz
-o spades_output
-t 16


## Align reads to assembly

bwa index spades_output/scaffolds.fasta
bwa mem -t 16 spades_output/scaffolds.fasta \
    trimmed_R1.fq.gz trimmed_R2.fq.gz | \
    samtools sort -@ 4 -o aligned.bam
samtools index aligned.bam

## Polish

pilon --genome spades_output/scaffolds.fasta \
    --frags aligned.bam \
    --output polished \
    --threads 16

Use cases

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