KHMER(1)

✨ KHMER(1) ✨

okay so bestie, welcome to the khmer manual page — it's giving k-mer counting, filtering and graph traversal FTW! 🧬💅

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🌸 NAME 🌸

khmer — k-mer counting, filtering and graph traversal FTW! 🎀

like literally, that's the whole name line. short. iconic. no notes. 👑

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🦋 SYNOPSIS 🦋

khmer `<prog_name>` [options] <args>

eg.

khmer `load-into-counting` -x 1e8 -k 20 reads.ct reads.fa.gz

that's the vibe. you call khmer, you give it a <prog_name>, you throw your [options] and your <args> at it, and it goes. ✨

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💖 USAGE 💖

okay so real talk: this manpage only describes the khmer wrapper script. that's it. that's the whole assignment. 🙈

if you actually wanna know about the software itself and how to use it, go look at /usr/share/doc/khmer or else http://khmer.readthedocs.org/. those are the places. go. shoo. 💫

so here's the thing about Debian/Ubuntu — on those, the package maintainers avoid putting big collections of scripts directly into the system PATH. understandable honestly. instead, a single wrapper script is used to launch the script you actually want. so if the khmer instructions tell you to run load-into-counting.py ...whatever..., you need to prefix this command with khmer. 🫶

and furthermore (love that word), the .py extension may be omitted, which is how you end up with a command in the format shown above. slay. 🌈

and if you don't like this? totally valid, bestie. simply add /usr/lib/khmer/bin to your personal PATH. problem solved, no cap. 💅

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🎀 AUTHOR 🎀

this wrapper and manpage were written by Tim Booth, who takes no credit for khmer itself. king behaviour, honestly — knows what he did and knows what he didn't. 🙇♀️⭐

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and that's the whole page!! the footer at the bottom just says KHMER(1) again with no date attached, which is so lowkey mysterious of it, but we move 💀 — anyways go count some k-mers, bestie, you're gonna eat 🔥👑