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bio-alignment-sorting

Maintainer FreedomIntelligence · Last updated April 1, 2026

Sort SAM/BAM files by coordinate or name with samtools sort.

OpenClawNanoClawAnalysisReproductionbio-alignment-sorting🧠 bioos extended suitebioos extended bioinformatics suitesort

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

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

Maintainer
FreedomIntelligence
License
MIT
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

  • Sort alignment files by coordinate or read name using samtools and pysam.
  • samtools sort -O bam -o sorted.bam input.bam.

Source Doc

Excerpt From SKILL.md

Sort Orders

OrderFlagUse Case
CoordinatedefaultIndexing, visualization, variant calling
Name-nPaired-end processing, fixmate, markdup
Tag-t TAGSort by specific tag value

Output as CRAM

samtools sort -O cram --reference ref.fa -o sorted.cram input.bam


## Sort by cell barcode (10x Genomics)

samtools sort -t CB -o sorted_by_barcode.bam input.bam

Use cases

  • Use bio-alignment-sorting for genomics and bioinformatics workflows.
  • Apply bio-alignment-sorting 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-indexing - Index after coordinate sorting
  • duplicate-handling - Requires name-sorted input for fixmate
  • alignment-filtering - Filter before or after sorting

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