AR
Data & Repro
Arboreto
Arboreto is a computational library for inferring gene regulatory networks (GRNs) from gene expression data using paralleli.
K-Dense-AI/claude-scientific-skillsView
Data & Repro
BI
bio-read-qc-umi-processing
Maintainer FreedomIntelligence · Last updated April 1, 2026
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.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-read-qc-umi-processing
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- CLI: umi_tools extract + umi_tools dedup (UMI-tools).
- CLI: fgbio GroupReadsByUmi + fgbio CallMolecularConsensusReads.
- Deduplicate reads using UMIs" → Extract UMI barcodes, group reads by UMI+position, and 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 library preparation to tag individual molecules before PCR amplification. This enables accurate PCR duplicate removal and 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.
Source Doc
Excerpt From SKILL.md
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 |
Use cases
- 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.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- 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
Related skills
Related skills
BI
Data & Repro
bio-imaging-mass-cytometry-cell-segmentation
Cell segmentation from multiplexed tissue images. Covers deep learning (Cellpose, Mesmer) and classical approaches for nuclear and whole-cel…
FreedomIntelligence/OpenClaw-Medical-SkillsView
BI
Data & Repro
bio-single-cell-batch-integration
Integrate multiple scRNA-seq samples/batches using Harmony, scVI, Seurat anchors, and fastMNN. Remove technical variation while preserving b…
FreedomIntelligence/OpenClaw-Medical-SkillsView
BI
Data & Repro
bio-single-cell-cell-annotation
Automated cell type annotation using reference-based methods including CellTypist, scPred, SingleR, and Azimuth for consistent, reproducible…
FreedomIntelligence/OpenClaw-Medical-SkillsView