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数据与复现
BI
bio-alignment-sorting
维护者 FreedomIntelligence · 最近更新 2026年4月1日
Sort SAM/BAM files by coordinate or name with samtools sort.
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-alignment-sorting
- 维护者
- FreedomIntelligence
- 许可
- MIT
- 最近更新
- 2026年4月1日
技能摘要
来自 SKILL.md 的关键信息
核心说明
- Sort alignment files by coordinate 或 read name ，使用 samtools 、 pysam。
- samtools sort -O bam -o sorted.bam input.bam。
原始文档
SKILL.md 摘录
Sort Orders
| Order | Flag | Use Case |
|---|---|---|
| Coordinate | default | Indexing, visualization, variant calling |
| Name | -n | Paired-end processing, fixmate, markdup |
| Tag | -t TAG | Sort 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
适用场景
- Use bio-alignment-sorting ，用于 genomics 、 bioinformatics workflows。
- Apply bio-alignment-sorting to sequencing，variant，或 omics analysis tasks。
不适用场景
- Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。
上游相关技能
- 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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