AA
AAV vector design: capsid selection, promoter optimization, payload capacity.
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数据与复现
BI
bio-clinical-databases-hla-typing
维护者 FreedomIntelligence · 最近更新 2026年4月1日
Call HLA alleles from NGS data using OptiType, HLA-HD, or arcasHLA for immunogenomics applications. Use when determining HLA genotype for transplant matching, neoantigen prediction, or pharmacogenomic screening.
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-clinical-databases-hla-typing
- 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
- CLI：OptiType ，用于 HLA class I typing ，面向 DNA/RNA reads。
- CLI：arcasHLA extract → arcasHLA genotype ，用于 RNA-seq based typing。
- Determine HLA genotype ，面向 my sequencing data" → Call HLA alleles ，面向 WGS/WES/RNA-seq reads ，用于 transplant matching，neoantigen prediction，或 pharmacogenomic screening. CLI：OptiType ，用于 HLA class I typing ，面向 DNA/RNA reads CLI：arcasHLA extract → arcasHLA genotype ，用于 RNA-seq based typing。
- samtools view -h input.bam chr6：28000000-34000000 | \ samtools fastq -1 hla_R1.fq -2 hla_R2.fq -。
原始文档
SKILL.md 摘录
OptiType (HLA Class I)
Goal: Call HLA Class I alleles (HLA-A, B, C) at 4-field resolution from WGS, WES, or RNA-seq data.
Approach: Extract HLA region reads from BAM, then run OptiType's integer linear programming algorithm to determine optimal allele assignment.
Run OptiType
OptiTypePipeline.py
-i hla_R1.fq hla_R2.fq
-d
-o optitype_output
-c config.ini
RNA mode
OptiTypePipeline.py
-i rna_R1.fq rna_R2.fq
-r
-o optitype_rna_output
-c config.ini
适用场景
- 适合在determining HLA genotype ，用于 transplant matching，neoantigen prediction，或 pharmacogenomic screening时使用。
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
- clinical-databases/pharmacogenomics - HLA-drug interactions
- variant-calling/clinical-interpretation - Clinical reporting
- single-cell/cell-type-annotation - HLA expression
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