SCI Skills

CN Directory
数据与复现临床医学与医药FreedomIntelligence/OpenClaw-Medical-Skills数据与复现
BI

bio-long-read-sequencing-clair3-variants

维护者 FreedomIntelligence · 最近更新 2026年4月1日

Deep learning-based variant calling from long reads using Clair3 for SNPs and small indels. Use when calling germline variants from ONT or PacBio alignments, particularly when high accuracy is needed for clinical or research applications.

OpenClawNanoClaw分析处理复现实验bio-long-read-sequencing-clair3-variants🧬 bioinformatics (gptomics bio-* suite)bioinformatics — sequencing & read qcdeep

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-long-read-sequencing-clair3-variants

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

2 min

核心说明

  • CLI：run_clair3.sh --bam_fn=sample.bam --ref_fn=ref.fa --平台=ont。
  • Call variants ，面向 my long-read data" → Use 深度学习 to identify germline SNPs 、 small indels ，面向 ONT 或 PacBio aligned reads ，支持 high accuracy. CLI：run_clair3.sh --bam_fn=sample.bam --ref_fn=ref.fa --平台=ont。
  • run_clair3.sh \ --bam_fn=sample.bam \ --ref_fn=reference.fasta \ --threads=32 \ --平台=ont \ --model_path=${CONDA_PREFIX}/bin/models/ont \ --output=clair3_output。

原始文档

SKILL.md 摘录

PacBio HiFi variant calling

run_clair3.sh
--bam_fn=sample.bam
--ref_fn=reference.fasta
--threads=32
--platform=hifi
--model_path=${CONDA_PREFIX}/bin/models/hifi
--output=clair3_output

Platform-Specific Models

PlatformModelRecommended Coverage
ONT R10r1041_e82_400bps_sup_v43030-60x
ONT R9r941_prom_sup_g501430-60x
PacBio HiFihifi20-40x
PacBio CLR-Use PEPPER-Margin-DeepVariant

## List available models

ls ${CONDA_PREFIX}/bin/models/

适用场景

  • 适合在calling germline variants ，面向 ONT 或 PacBio alignments，particularly when high accuracy is needed ，用于 clinical 或 research applications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

  • variant-calling/bcftools-basics - VCF manipulation
  • variant-calling/filtering-best-practices - Quality filtering
  • long-read-sequencing/long-read-qc - Input quality control
  • long-read-sequencing/long-read-alignment - Mapping with minimap2

相关技能

相关技能

返回目录
AR
数据与复现临床医学与医药

armored-cart-design-agent

Design armored CAR-T cells with cytokine payloads and resistance mechanisms.

OpenClawNanoClaw分析处理
FreedomIntelligence/OpenClaw-Medical-Skills查看
AR
数据与复现临床医学与医药

arxiv-search

Search arXiv physics, math, and computer science preprints using natural language queries. Powered by Valyu semantic sea…

OpenClawNanoClaw分析处理
FreedomIntelligence/OpenClaw-Medical-Skills查看
AU
数据与复现临床医学与医药

autonomous-oncology-agent

Autonomous oncology research agent: literature mining, trial matching, biomarker analysis, and treatment hypothesis gene…

OpenClawNanoClaw分析处理
FreedomIntelligence/OpenClaw-Medical-Skills查看
BI
数据与复现临床医学与医药

bio-cfdna-preprocessing

Preprocesses cell-free DNA sequencing data including adapter trimming, alignment optimized for short fragments, and UMI-…

OpenClawNanoClaw分析处理
FreedomIntelligence/OpenClaw-Medical-Skills查看