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bio-read-alignment-hisat2-alignment

95 / 100 · Low risk

Fine to try.

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

Aligns RNA-seq reads to a genome with HISAT2, the splice-aware aligner whose hierarchical graph FM-index runs at roughly a quarter of STAR's memory (~7 GB for human), whose SNP/haplotype graph index reduces reference bias in the index itself, and whose MAPQ is GATK-friendly (60 for unique, no 255 problem). Use when RNA alignment must fit a memory-constrained machine, when feeding StringTie/Cufflinks transcript assembly via --dta, or when a SNP-aware graph index is wanted for allele-robust mappi…

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-read-alignment-hisat2-alignment' ] || [ -L ~/.agents/skills/'bio-read-alignment-hisat2-alignment' ]; then echo 'A skill folder named bio-read-alignment-hisat2-alignment 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 "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/bio-read-alignment-hisat2-alignment' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bio-read-alignment-hisat2-alignment' ~/.agents/skills/'bio-read-alignment-hisat2-alignment' && 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-read-alignment-hisat2-alignment' ~/.claude/skills/'bio-read-alignment-hisat2-alignment' (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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