SIMPLE(1)

💖 SIMPLE(1) 💖

okay bestie, welcome to the manual for simple — she's a User Command and she's about to change your whole kmer-counting life, no cap. 🦋

✨ NAME ✨

simple — the obvious array-based kmer counter 👑

✨ SYNOPSIS ✨

simple [-f|-r|-C] [-c compression] [-m mersize] -i input -o output

✨ DESCRIPTION ✨

so. simple is literally a very simple mer counter. that's the whole vibe. 💅

here's the tea: she allocates one gigantic 32-bit array, populates that array with mers, sorts, and then writes the output. that's it. that's the whole main character arc. ✨

⚠️ bestie. listen. she will allocate 4 bytes per kmer. so k=16 will require 16 GB to run. sixteen. gigabytes. not me casually asking your RAM for its entire personality. 😭

✨ OPTIONS ✨

• -i input — your input, bestie 🫶
• -o output — where the output goes, slay 💖
• -m mersize — the mer size. Default is 22 ⭐
• -f — forward kmer (this is the default) 💅
• -r — reverse kmer 🔄
• -C — canonical kmer (lexicographically smaller of the forward and reverse kmer at each location) 👑
• -c # — mer compression 🌸

✨ SEE ALSO ✨

• meryl(1)

and that's the whole page, periodt. 🎀

this lil manual is from simple 0~20150520+2004, dated May 2015 — so yeah, she's vintage, she's iconic, she's been holding it down since way back. 🌈 go forth and count your kmers, bestie. 💜🧚