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bio-read-alignment-bowtie2-alignment

Maintainer FreedomIntelligence · Last updated April 1, 2026

Align short reads with Bowtie2; local and end-to-end modes.

OpenClawNanoClawAnalysisReproductionbio-read-alignment-bowtie2-alignment🧠 bioos extended suitebioos extended bioinformatics suitealign

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-read-alignment-bowtie2-alignment

Maintainer
FreedomIntelligence
License
MIT
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

  • bowtie2-build reference.fa reference_index.
  • bowtie2-build --threads 8 reference.fa reference_index.

Source Doc

Excerpt From SKILL.md

Paired-end reads

bowtie2 -p 8 -x reference_index -1 reads_1.fq.gz -2 reads_2.fq.gz -S aligned.sam

Single-end reads

bowtie2 -p 8 -x reference_index -U reads.fq.gz -S aligned.sam

Direct to sorted BAM

bowtie2 -p 8 -x reference_index -1 r1.fq.gz -2 r2.fq.gz |
samtools sort -@ 4 -o aligned.sorted.bam -

Use cases

  • Use bio-read-alignment-bowtie2-alignment for genomics and bioinformatics workflows.
  • Apply bio-read-alignment-bowtie2-alignment 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

  • read-qc/fastp-workflow - Preprocess reads before alignment
  • alignment-files/alignment-sorting - Post-alignment processing
  • chip-seq/peak-calling - ChIP-seq analysis
  • atac-seq/atac-peak-calling - ATAC-seq analysis

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