AR
数据与复现
Arboreto
Arboreto is a computational library for inferring gene regulatory networks (GRNs) from gene expression data using parall…
K-Dense-AI/claude-scientific-skills查看
数据与复现
BI
bio-read-qc-umi-processing
维护者 FreedomIntelligence · 最近更新 2026年4月1日
Extract, process, and deduplicate reads using Unique Molecular Identifiers (UMIs) with umi_tools. Use when library prep includes UMIs and accurate molecule counting is needed, such as in single-cell RNA-seq, low-input RNA-seq, or targeted sequencing to distinguish PCR from biological duplicates.
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-read-qc-umi-processing
- 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：umi_tools extract + umi_tools dedup (UMI-tools)。
- CLI：fgbio GroupReadsByUmi + fgbio CallMolecularConsensusReads。
- Deduplicate reads ，使用 UMIs" → Extract UMI barcodes，group reads by UMI+position，、 collapse PCR duplicates to count unique molecules. CLI：umi_tools extract + umi_tools dedup (UMI-tools) CLI：fgbio GroupReadsByUmi + fgbio CallMolecularConsensusReads。
- UMIs (Unique Molecular Identifiers) are short random sequences added during 库 preparation to tag individual molecules before PCR amplification. This enables accurate PCR duplicate removal 、 molecule counting。
- umi_tools extract \ --stdin=R1.fastq.gz \ --read2-in=R2.fastq.gz \ --stdout=R1_extracted.fastq.gz \ --read2-out=R2_extracted.fastq.gz \ --bc-pattern=NNNNNNNN。
原始文档
SKILL.md 摘录
UMI at start of R2
umi_tools extract
--stdin=R1.fastq.gz
--read2-in=R2.fastq.gz
--stdout=R1_extracted.fastq.gz
--read2-out=R2_extracted.fastq.gz
--bc-pattern2=NNNNNNNN
UMI in both reads
umi_tools extract
--stdin=R1.fastq.gz
--read2-in=R2.fastq.gz
--stdout=R1_extracted.fastq.gz
--read2-out=R2_extracted.fastq.gz
--bc-pattern=NNNNNNNN
--bc-pattern2=NNNNNNNN
## UMI Pattern Syntax
| Pattern | Meaning |
|---------|---------|
| `N` | UMI base (extracted) |
| `C` | Cell barcode (extracted, kept separate) |
| `X` | Discard base |
| `NNNNNNNN` | 8bp UMI |
| `CCCCCCCCNNNNNNNN` | 8bp cell barcode + 8bp UMI |
| `NNNXXXNNN` | 3bp UMI, skip 3bp, 3bp UMI |
适用场景
- 适合在库 prep includes UMIs 、 accurate molecule counting is needed，such as in single-cell RNA-seq，low-input RNA-seq，或 targeted sequencing to distinguish PCR ，面向 biological duplicates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
- fastp-workflow - Simple UMI extraction during preprocessing
- quality-filtering - QC before UMI extraction
- alignment-files/sam-bam-basics - BAM sorting/indexing required before dedup
- single-cell/preprocessing - scRNA-seq workflows use UMI counting
相关技能
相关技能
Cell segmentation from multiplexed tissue images. Covers deep learning (Cellpose, Mesmer) and classical approaches for n…
FreedomIntelligence/OpenClaw-Medical-Skills查看
Integrate multiple scRNA-seq samples/batches using Harmony, scVI, Seurat anchors, and fastMNN. Remove technical variatio…
FreedomIntelligence/OpenClaw-Medical-Skills查看
Automated cell type annotation using reference-based methods including CellTypist, scPred, SingleR, and Azimuth for cons…
FreedomIntelligence/OpenClaw-Medical-Skills查看