bio-read-qc-umi-processing
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.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-read-qc-umi-processing --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: pandas 2.2+, samtools 1.19+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # UMI Processing **"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 Workflow Overview ``` Raw FASTQ with UMIs | v [umi_tools extract] --> Move UMI to read header | v [Alignment] --> bwa/STAR/bowtie2 | v [umi_tools dedup] --> Remove PCR duplicates based on UMI + position | v Deduplicated
- Version Compatibility
- UMI Workflow Overview
- Extract UMIs from Reads
- UMI in Read Sequence
- UMI Pattern Syntax
- Complex Patterns
- UMI in Separate Index Read
- Quality Filtering During Extraction
- Deduplication
- Basic Deduplication
- Deduplication Methods
- Method Selection Guide
- Paired-End Deduplication
- Gene-Level Deduplication
UMI at start of R1 (8bp UMI) umi_tools extract \ UMI at start of R2 UMI in both reads Skip bases between barcode and UMI Fixed anchor sequence UMI in I1 index read Filter by UMI quality Filter UMIs with N bases Must be sorted and indexed first
What does the bio-read-qc-umi-processing skill do?
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.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-read-qc-umi-processing --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.