KRAKEN-FILTER(1)

💖 KRAKEN-FILTER 💖

okay bestie, welcome to kraken-filter</>, section 1 of the User Commands manual. yes it's that kraken-filter. no it is not the sea monster. (well. spiritually maybe.) 🦑✨

🌸 NAME 🌸

kraken-filter — assigning taxonomic labels to short DNA sequences

that's the whole pitch. short DNA sequences, taxonomic labels, assigned. iconic behaviour honestly. 💅

✨ SYNOPSIS ✨

kraken-filter [--db KRAKEN_DB_NAME] [--threshold NUM] <kraken output file(s)>

so the vibe is: you hand it one or more kraken output files (that's the <kraken output file(s)> part, and yes you can pass more than one, slay), you can optionally point it at a database with --db KRAKEN_DB_NAME, and you can optionally set a number with --threshold NUM. both options are in square brackets which means optional, but the output file(s) are not, so don't come to class empty-handed. 🎀

🦋 DESCRIPTION 🦋

so bestie… the manual page itself literally has nothing here. not a single line of description. i checked. i looked. it's just vibes and empty space. 😭

what we do know from the NAME section is that kraken-filter is about assigning taxonomic labels to short DNA sequences. that's it. that's the lore. i am not about to sit here and make up extra behaviour for you, because that would be lying to my bestie and i would never. 🙈

fr fr: if you need more than this page gives you, the page is the problem, not you. run the command's own --help if it has one, or go read the actual docs. no cap. 💀

👑 THE OPTIONS, AS PROMISED 👑

they're short but they're mighty:

• --db KRAKEN_DB_NAME — you give it a kraken database name. it's written KRAKEN_DB_NAME in the synopsis and that's a placeholder, so swap in your actual db name, bestie. 🫶
• --threshold NUM — you give it a number. NUM. that's the placeholder. the manpage does not say what the number does, so i'm not gonna pretend i know, and neither should anyone else at this party. 🌈

and that's literally all of them. two options. a whole tool. minimalism ate. ⭐

🧚 A TINY REMINDER 🧚

the synopsis is the whole contract here, so let's say it one more time, nice and clean:

kraken-filter [--db KRAKEN_DB_NAME] [--threshold NUM] <kraken output file(s)>

copy it, paste it, swap the placeholders for your real values, and go assign those taxonomic labels to those short DNA sequences like the main character you are. 💜

that's the page!! written in September 2015 for kraken-filter version 0.10.5~beta — yeah it's a beta and yeah it's a little vintage, but we love her anyway. go forth and filter, bestie. mwah. 🍓💖✨