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bio-long-read-sequencing-clair3-variants

95 / 100 · Low risk

Fine to try.

By lilinji/GeneTind-Life-Skills (GitHub) · other · 17 stars · scanned at commit 908229c

Calls germline small variants (SNPs and indels) from Oxford Nanopore and PacBio HiFi long reads with Clair3, a two-stage (pileup + full-alignment) deep-learning caller, selecting the chemistry- and basecaller-version-matched model, enabling read-based phasing, and benchmarking against GIAB with stratification. Covers why the model string is the experiment (no auto-detection, silent degradation on mismatch), why ONT homopolymer/STR indels are the residual error whole-genome F1 hides, and the som…

Works with any agent that supports SKILL.md skills.

What this skill can do

Install

Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.

if [ -e ~/.agents/skills/'bio-long-read-sequencing-clair3-variants' ] || [ -L ~/.agents/skills/'bio-long-read-sequencing-clair3-variants' ]; then echo 'A skill folder named bio-long-read-sequencing-clair3-variants already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/lilinji/GeneTind-Life-Skills' "$d" && git -C "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/bio-long-read-sequencing-clair3-variants' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bio-long-read-sequencing-clair3-variants' ~/.agents/skills/'bio-long-read-sequencing-clair3-variants' && rm -rf "$d"; fi

Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'bio-long-read-sequencing-clair3-variants' ~/.claude/skills/'bio-long-read-sequencing-clair3-variants' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.

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