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FreedomIntelligence/OpenClaw-Medical-SkillsView
Data & Repro
BI
bio-long-read-sequencing-isoseq-analysis
Maintainer FreedomIntelligence · Last updated April 1, 2026
Analyze PacBio Iso-Seq data for full-length isoform discovery and quantification. Use when characterizing transcript diversity or identifying novel splice variants.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-long-read-sequencing-isoseq-analysis
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- CLI: isoseq3 refine → isoseq3 cluster → pbmm2 align → sqanti3_qc.py.
- 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.
- ccs input.subreads.bam ccs.bam \ --min-rq 0.9 \ --min-passes 3 \ --num-threads 32.
Source Doc
Excerpt From SKILL.md
Iso-Seq specific primer removal
lima ccs.bam primers.fasta demux.bam
--isoseq
--peek-guess
--num-threads 16
Remove polyA tails and concatemers
isoseq3 refine demux.primer_5p--primer_3p.bam primers.fasta refined.bam
--require-polya
--min-polya-length 20
Check refinement stats
cat refined.filter_summary.json | jq
Use cases
- Use when characterizing transcript diversity or identifying novel splice variants.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- long-read-sequencing/basecalling - ONT/PacBio basics
- rna-quantification/alignment-free-quant - Expression analysis
- genome-intervals/gtf-gff-handling - GTF/GFF handling
- differential-expression/timeseries-de - Differential isoform usage
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