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bio-long-read-sequencing-medaka-polishing

95 / 100 · Low risk

Fine to try.

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

Polishes Oxford Nanopore draft assemblies to higher consensus accuracy with medaka, a basecaller-model-specific neural consensus net, produces haploid variant calls (VCF) for microbial, mitochondrial, or viral samples, and generates amplicon/viral consensus sequences. Covers the model-matching footgun that silently degrades output, why Racon-first is obsolete and medaka runs directly on Flye output as a single pass, why HiFi must never be fed to medaka, the v1->v2 subcommand renames, and the pr…

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