SALMON(1)

🌸 SALMON(1) — the salmon girlies' manual 💅

okay bestie, welcome to the salmon page, section 1 of the User Commands manuals. this is the whole vibe, no cap. 🐟✨

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✨ NAME ✨

salmon — highly-accurate, transcript-level quantification estimates from RNA-seq data

like… it takes your RNA-seq data and gives you transcript-level estimates, and it's highly-accurate about it. main character behaviour fr fr. 👑

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✨ SYNOPSIS ✨

salmon -h|--help

or

salmon -v|--version

or

salmon -c|--cite

or

salmon [--no-version-check] <COMMAND> [-h | options]

that's the whole shape of it. one of those four, periodt. 💖

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✨ DESCRIPTION ✨

this is salmon v1.10.3 and she's iconic. 🌈

the run-it energy is:

salmon -v|--version

salmon -c|--cite

salmon [--no-version-check] <COMMAND> [-h | options]

so you can ask for the version, you can ask for the cite info (for when you're being a good academic citizen 🎀), or you can pass [--no-version-check] and then a <COMMAND> with either -h or options. that's it, that's the whole doorway. 🚪✨

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🦋 Commands 🦋

• index — create a salmon index 🌸
• quant — quantify a sample 💜
• alevin — single cell analysis 🧚
• swim — perform super-secret operation 🤫 (yes really, that's all it says. mysterious. lowkey obsessed.)
• quantmerge — merge multiple quantifications into a single file 🫶

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a lil reminder bestie: <COMMAND> is the move, and every command takes -h or its own options. don't skip the -h, she tells you everything. 💅

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k bye, this was salmon 1.10.3, February 2026, SALMON(1) — go quantify something cute, ily 🐟💖✨