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bio-read-alignment-hisat2-alignment

Maintainer FreedomIntelligence · Last updated April 1, 2026

Splice-aware RNA-seq alignment with HISAT2.

OpenClawNanoClawAnalysisReproductionbio-read-alignment-hisat2-alignment🧠 bioos extended suitebioos extended bioinformatics suitesplice

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-read-alignment-hisat2-alignment

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

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

hisat2-build -p 8 reference.fa hisat2_index.
hisat2_extract_splice_sites.py annotation.gtf > splice_sites.txt hisat2_extract_exons.py annotation.gtf > exons.txt.
hisat2-build -p 8 \ --ss splice_sites.txt \ --exon exons.txt \ reference.fa hisat2_index.

Source Doc

Excerpt From SKILL.md

Paired-end reads

hisat2 -p 8 -x hisat2_index
-1 reads_1.fq.gz -2 reads_2.fq.gz
-S aligned.sam

Single-end reads

hisat2 -p 8 -x hisat2_index
-U reads.fq.gz
-S aligned.sam


## Pipe to samtools

hisat2 -p 8 -x hisat2_index \
    -1 r1.fq.gz -2 r2.fq.gz | \
    samtools sort -@ 4 -o aligned.sorted.bam -

samtools index aligned.sorted.bam

Use cases

Use bio-read-alignment-hisat2-alignment for genomics and bioinformatics workflows.
Apply bio-read-alignment-hisat2-alignment to sequencing, variant, or omics analysis tasks.