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bio-long-read-sequencing-nanopore-methylation

95 / 100 · Low risk

Fine to try.

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

Calls DNA base modifications (5mC, 5hmC, 6mA, 4mC) directly from Oxford Nanopore and PacBio HiFi long reads encoded as MM/ML SAM tags, piles them into per-site bedMethyl with modkit (or pb-CpG-tools for PacBio), and produces phased allele-specific methylation. Covers why methylation is a basecalling decision that cannot be recovered later, the MM/ML tag-drop failure that silently zeroes methylation through alignment, the MM ? vs . no-call semantics, 5mC/5hmC resolution vs bisulfite, modkit's 10…

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-nanopore-methylation' ] || [ -L ~/.agents/skills/'bio-long-read-sequencing-nanopore-methylation' ]; then echo 'A skill folder named bio-long-read-sequencing-nanopore-methylation 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 "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/bio-long-read-sequencing-nanopore-methylation' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bio-long-read-sequencing-nanopore-methylation' ~/.agents/skills/'bio-long-read-sequencing-nanopore-methylation' && 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-nanopore-methylation' ~/.claude/skills/'bio-long-read-sequencing-nanopore-methylation' (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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