Claude Code
Codex
Cursor
GitHub Copilot
Gemini CLIAbout this skill
Aligns Oxford Nanopore and PacBio long reads (and assemblies) to a reference with minimap2 using the error-rate-matched preset (map-ont, lr:hq, map-hifi, map-pb, splice/splice:hq, asm5/10/20, ava), producing a sorted/indexed BAM for variant, SV, methylation, or isoform analysis. Covers why the preset rewrites the scoring/chaining model, why SV calling rides on supplementary not secondary alignments, carrying MM/ML methylation tags through with -y, the multi-part-index MAPQ trap, and when to swap in Winnowmap/VACmap/lra/pbmm2. Use when mapping ONT or PacBio reads, choosing a minimap2 preset by platform/chemistry, preparing input for Clair3/medaka/Sniffles/modkit, aligning into repeats/centromeres, or spliced-aligning cDNA/Iso-Seq.
Quick start
- Copy the install prompt. Use the green button above this README.
- Send it to your agent. Paste it into your coding agent’s chat and send.
- Review the setup. Your agent checks the skill’s instructions, requirements, and installation scope.
Review, license & listing details
This is an imported listing. We haven’t certified its safety, license, or compatibility. Skills may include executable scripts.
Only SKILL.md was scanned. Supporting files and scripts were not checked. No safety grade has been assigned.
0 potential findings · Scanned 11/4/2026 · Scanner 0.2.1
Content SHA-256: 305d0fd6de708c98c1577e937465c929886010e3efd4136e088d8552d32f22fa
About this listing
- Category
- Science & research
- Reported license
- Not specified
- Listing language (estimated)
- English
- Review status
- Not individually reviewed
- Agent compatibility
- Atlas installation supports Claude Code, Codex, and Cursor. Skill-specific dependencies and features are checked during setup.