Bio Long Read Sequencing Long Read Alignment
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.
Security AStatic scan found no risk patternsHow grading works ›
What this skill does
Bio Long Read Sequencing Long Read Alignment is a community-contributed Claude Code skill in the chemistry sub-category. It ships as a SKILL.md file that Claude Code auto-discovers under ~/.claude/skills/bio-long-read-sequencing-long-read-alignment/ and loads when your prompt matches the skill's trigger.
When to invoke it: 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.
Who uses this skill
The Bio Long Read Sequencing Long Read Alignment Claude Code skill is built for researchers, data scientists, academics, and analysts working with complex data and scientific literature. It's part of ClaudSkills (also referred to as Claude Skills or Claude Code Skills) — the open community-curated registry of 161,000+ SKILL.md files for Anthropic's Claude Code agent and the wider Claude ecosystem (Claude API, Claude Agent SDK).
How to install
Free
Manual install (2 steps)
mkdir -p ~/.claude/skills/bio-long-read-sequencing-long-read-alignment
curl -L https://claudskills.com/skills/bio-long-read-sequencing-long-read-alignment/SKILL.md \
-o ~/.claude/skills/bio-long-read-sequencing-long-read-alignment/SKILL.md
Or just download SKILL.md directly and drop it into ~/.claude/skills/bio-long-read-sequencing-long-read-alignment/. Claude Code auto-discovers it on next session.
Skills live at ~/.claude/skills/bio-long-read-sequencing-long-read-alignment/SKILL.md on macOS/Linux, or %USERPROFILE%\.claude\skills\bio-long-read-sequencing-long-read-alignment\SKILL.md on Windows. See the full install guide for step-by-step instructions.
Telegram
📱 Install from your phone or desktop Telegram
Open @claudskills_bot on Telegram, tap Open Desktop App, and the desktop app installs this skill for you. Or share the bot link with a colleague — they get the same one-tap install. Learn more →
Pro
One-click install via the desktop app
The ClaudSkills desktop app installs any skill directly into ~/.claude/skills/ with one click — no terminal required. Pro starts at $9/mo or $149 lifetime.
Pro
For the full experience including quality scoring and one-click install features for each skill — upgrade to Pro.
Frequently asked questions
How do I install the Bio Long Read Sequencing Long Read Alignment Claude Code skill?
Install via the ClaudSkills desktop app (one click) or copy
SKILL.md from the source repository to
~/.claude/skills/bio-long-read-sequencing-long-read-alignment/SKILL.md and restart Claude Code. Both flows are detailed at
claudskills.com/install/.
What does the Bio Long Read Sequencing Long Read Alignment skill do?
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.
Is this skill free to install?
Yes. ClaudSkills is an open registry — every skill keeps its source repository's license, and manual install via copy is free. ClaudSkills Pro ($9/mo, $79/yr, or $149 one-time) adds one-click install via the desktop app and a multi-signal Quality Score.
When should I use the Bio Long Read Sequencing Long Read Alignment skill?
Use Bio Long Read Sequencing Long Read Alignment when your Claude Code task falls under the Science & Research category — specifically in the chemistry area. Claude Code auto-discovers installed skills and invokes the right one based on the task description, so you can also ask Claude directly (e.g. "use Bio Long Read Sequencing Long Read Alignment" or describe the task and let Claude pick). Browse related skills at
/category/science/.
What is a Claude Code skill and how does the Bio Long Read Sequencing Long Read Alignment skill fit in?
A Claude Code skill is a
SKILL.md file that lives under
~/.claude/skills/<name>/ and tells the Claude Code CLI agent how to perform a specific task (instructions, prompts, allowed tools). Skills are auto-discovered at session start. Bio Long Read Sequencing Long Read Alignment is one of 67,000+ skills indexed in the open ClaudSkills catalog, classified under the Science & Research category. Learn more at
/learn/what-is-a-claude-skill/.
Attribution & license
Cite this skill
If you reference this skill in a blog post, paper, or documentation, you can cite it as:
APA
bg-szy. (2026). Bio Long Read Sequencing Long Read Alignment [Claude Code skill]. ClaudSkills. https://claudskills.com/skills/bio-long-read-sequencing-long-read-alignment/
BibTeX
@misc{bio-long-read-sequencing-long-read-alignment-2026,
author = {bg-szy},
title = {Bio Long Read Sequencing Long Read Alignment [Claude Code skill]},
year = {2026},
publisher = {ClaudSkills},
url = {https://claudskills.com/skills/bio-long-read-sequencing-long-read-alignment/}
}Embed this skill
Promote, attribute, or link this skill from your own README, blog post, or documentation. All three snippets are free to use — no sign-up, no API key. More distribution surfaces →
Badge
[](https://claudskills.com/skills/bio-long-read-sequencing-long-read-alignment/?utm_source=badge&utm_medium=readme&utm_campaign=skill_badge)
<script>
<script src="https://claudskills.com/embed/bio-long-read-sequencing-long-read-alignment.js" async></script>
<iframe>
<iframe src="https://claudskills.com/embed/bio-long-read-sequencing-long-read-alignment.html" width="100%" height="160" frameborder="0" loading="lazy" title="ClaudSkills: Bio Long Read Sequencing Long Read Alignment"></iframe>
Security scan
Grade A · scanned 2026-07-26 — free static scan against the OWASP Agentic Skills Top 10.
No risk patterns were found in any of the ten OWASP-aligned categories. How grading works ›
- ✓ Prompt injection
- ✓ Data exfiltration
- ✓ Supply chain
- ✓ Reverse shell
- ✓ Credentials
- ✓ Execution
- ✓ Filesystem
- ✓ Persistence
- ✓ Obfuscation
- ✓ Network
Show this grade on your repo (click to copy):
[](https://claudskills.com/skills/bio-long-read-sequencing-long-read-alignment/#security)
More Science & Research skills
Browse all Science & Research skills in the ClaudSkills registry, or explore these other picks from the same category:
Part of Acreator Store — Adam Lankamer's AI tools:
PerfectStudio ·
Ucaption ·
UTagger ·
AutoXPoster ·
TestYourSkills ·
AutomationFlows ·
Au Naturel ·
Telegram @acreatorstore