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Data & ReproBioinformatics & GenomicsFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction
BI

bio-alignment-indexing

Maintainer FreedomIntelligence · Last updated April 1, 2026

Index BAM/CRAM files with samtools index for random access.

OpenClawNanoClawAnalysisReproductionbio-alignment-indexing🧠 bioos extended suitebioos extended bioinformatics suiteindex

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

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

Maintainer
FreedomIntelligence
License
MIT
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

  • Create indices for random access to alignment files using samtools and pysam.
  • samtools view -H input.bam | grep "^@HD.

Source Doc

Excerpt From SKILL.md

Index Types

IndexExtensionUse Case
BAI.baiStandard BAM index, chromosomes < 512 Mbp
CSI.csiLarge chromosomes, custom bin sizes
CRAI.craiCRAM index

Create BAI Index

samtools index input.bam

## Create CSI Index

```bash
samtools index -c input.bam

Use cases

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

  • sam-bam-basics - View and convert alignment files
  • alignment-sorting - Sort BAM files (required before indexing)
  • alignment-filtering - Filter by regions using index
  • bam-statistics - Use idxstats for quick counts
  • sequence-io/read-sequences - Index FASTA with SeqIO.index_db()

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