bio-long-read-sequencing-isoseq-analysis
Analyze PacBio Iso-Seq data for full-length isoform discovery and quantification. Use when characterizing transcript diversity or identifying novel splice variants.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-long-read-sequencing-isoseq-analysis --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: minimap2 2.26+, pandas 2.2+, pysam 0.22+, 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 - R: `packageVersion('<pkg>')` then `?function_name` to verify parameters - 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. # Iso-Seq Analysis **"Analyze full-length isoforms from my Iso-Seq data"** → Process PacBio HiFi reads through CCS generation, primer removal, clustering, and isoform classification to discover novel transcript variants. - CLI: `isoseq3 refine` → `isoseq3 cluster` → `pbmm2 align` → `sqanti3_qc.py` ## IsoSeq3 Pipeline Overview ```bash # Full pipeline: subreads -> HQ transcripts # 1. CCS: Generate circular consensus sequences # 2. Lima: Remove primers and demultiplex # 3. Refine: Remove polyA and concatemers # 4. Cluster: Group into isoforms # 5. Polish: Generate high-quality consensus (optional with HiFi) ``` ## CCS Gener
- Version Compatibility
- IsoSeq3 Pipeline Overview
- CCS Generation
- Primer Removal with Lima
- Primer File Format
- Refine Full-Length Reads
- Cluster Into Isoforms
- Align to Reference
- Collapse Redundant Isoforms
- SQANTI3 Quality Control
- SQANTI3 Categories
- SQANTI3 Filtering
- Quantification with Pigeon
- TAMA for Annotation Merge
Full pipeline: subreads -> HQ transcripts Generate CCS from subreads (skip if using HiFi reads) ccs input.subreads.bam ccs.bam \ For HiFi reads, CCS is already done Start directly from HiFi reads Iso-Seq specific primer removal lima ccs.bam primers.fasta demux.bam \ Lima reports also contain demux statistics Check lima report cat demux.lima.summary
What does the bio-long-read-sequencing-isoseq-analysis skill do?
Analyze PacBio Iso-Seq data for full-length isoform discovery and quantification. Use when characterizing transcript diversity or identifying novel splice variants.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-long-read-sequencing-isoseq-analysis --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.