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long-read-sequencing-agent
Maintainer FreedomIntelligence · Last updated April 1, 2026
Long-read sequencing analysis: SV calling, methylation, isoform discovery, assembly.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/long-read-sequencing-agent
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- The Long-Read Sequencing Agent provides comprehensive AI-driven analysis of long-read sequencing data from PacBio (HiFi) and Oxford Nanopore (ONT) platforms. It enables structural variant detection, full-length isoform discovery, base modification calling, and de novo genome assembly.
- When detecting structural variants (SVs) missed by short-read sequencing.
- To characterize full-length transcript isoforms and alternative splicing.
- For detecting DNA base modifications (5mC, 6mA) directly from sequencing.
- When performing de novo genome assembly for complex regions.
Source Doc
Excerpt From SKILL.md
Core Capabilities
-
Structural Variant Detection: AI-enhanced SV calling for deletions, insertions, inversions, translocations, and complex rearrangements.
-
Isoform Discovery: Full-length transcript sequencing for novel isoform and fusion detection.
-
Base Modification Calling: Direct detection of DNA methylation (5mC, 5hmC, 6mA) from native sequencing.
-
Haplotype Phasing: Phase-resolved assemblies and variant calling.
-
De Novo Assembly: Assemble complex genomic regions (centromeres, telomeres, HLA).
-
Error Correction: AI-based error correction for long-read data.
Platform Comparison
| Feature | PacBio HiFi | ONT (R10+) |
|---|---|---|
| Read length | 15-25 kb | >100 kb possible |
| Accuracy | >99.9% (HiFi) | >99% (Q20+) |
| Base mods | 5mC, 6mA | 5mC, 5hmC, 6mA, more |
| Throughput | 20-40 Gb/run | 100+ Gb/run |
| Cost | Higher | Lower |
Workflow
-
Input: Long-read FASTQ/BAM files from PacBio or ONT sequencing.
-
QC & Alignment: Filter reads by quality, align to reference genome.
-
SV Calling: Detect structural variants using Sniffles, PBSV, or CuteSV.
-
Isoform Analysis: Identify full-length isoforms with IsoSeq or FLAIR.
-
Modification Calling: Extract base modifications from signal data.
-
Phasing: Generate haplotype-resolved variant calls.
-
Output: SV calls, isoform annotations, modification maps, phased assemblies.
Use cases
- When detecting structural variants (SVs) missed by short-read sequencing.
- To characteri.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- Long_Read_SV_Caller - For specialized SV analysis
- Variant_Interpretation - For variant annotation
- Epigenomics_MethylGPT_Agent - For methylation analysis
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