KMA_INDEX(1)

✨ kma_index ✨

okay so bestie, welcome to kma_index — a lil User Commands girly whose whole job is setting you up before the real main character (KMA) shows up. 💅

🌸 NAME 🌸

kma_index — creates the databases needed to run KMA, from a list of fasta files given 🦋

💖 DESCRIPTION 💖

so basically: kma_index creates the databases needed to run KMA, from a list of fasta files given. that's the whole vibe. it's giving "prep era before the glow-up." ✨

and then, the options, bestie. the original page lays them out as an options/description/defaults situation, so here they are, all of them, no skips, no crumbs left behind 👑

• -i — the input/query file name. you can hand it STDIN by passing "--". default: None
• -o — the output file. default: the input/template file 🫶
• -batch — the batch input file
• -deCon — the file with contamination. you can pass "--" for STDIN. default: None/False
• -batchD — the batch decon file
• -t_db — add to an existing DB. default: None/False
• -k — kmersize. default: 16
• -k_t — kmersize for template identification. default: 16
• -k_i — kmersize for indexing. default: 16
• -ML — minimum length of templates. default: kmersize (16)
• -CS — start chain size. default: 1 M
• -ME — mega DB. default: False
• -NI — do not dump *.index.b. default: False
• -Sparse — make a sparse DB. you can pass '-' for no prefix. default: None/False
• -ht — homology template. default: 1.0
• -hq — homology query. default: 1.0
• -and — both homology thresholds have to be reached. (the page also ends this one with a lone or — no explanation, no context, we simply respect the mystery 💀)
• -nbp — no bias print. default: False
• -v — version 👑
• -h — shows this help message 🎀

🎀 AUTHOR 🎀

this manpage was written by Nilesh Patra for the Debian distribution, and can be used for any other usage of the program. periodt. 💜

sign-off moment: this whole page is kma_index version 1.3.23, dated July 2021, and it lives in the KMA_INDEX(1) manual. slay, bye bestie 🦋💖✨