KRAKEN2(1)

✨ KRAKEN2 ✨ (that's the kraken2 manual page, bestie 💅)

okay so real talk — kraken2 is the girl who assigns taxonomic labels to short DNA sequences. yes, that's the whole job. she looks at your little DNA reads and goes "mmm this one's from this organism, periodt" 🌸

🦋 SYNOPSIS 🦋

kraken2 [options] <filename(s)>

that's it. options, then your files. iconic.

💖 OPTIONS 💖

okay here's the whole menu, no skips, no cuts, we're doing all of them 🫶

• --db NAME — the name for your Kraken 2 DB. default: none (so like… set this, bestie 😭)
• --threads NUM — how many threads you want. default: 1. give her more threads, she deserves it ⭐
• --quick — quick operation mode: use the first hit or hits and dip. no overthinking, main character energy.
• --unclassified-out FILENAME — print unclassified sequences to a filename. the ones that didn't get a label go live here.
• --classified-out FILENAME — print classified sequences to a filename. the ones that did get a label, slay.
• --output FILENAME — print output to a filename. default is stdout; and heads up, "-" will suppress normal output entirely.
• --confidence FLOAT — confidence score threshold. default: 0.0. and she must be in [0, 1] — no funny business 💀
• --minimum-base-quality NUM — minimum base quality used in classification. default: 0. lowkey only effective with FASTQ input, so don't come for her if your format isn't FASTQ 🙈
• --report FILENAME — print a report with aggregrate counts/clade to file. (yes, "aggregrate", that's how it's spelled here, we don't edit the queen 👑)
• --use-mpa-style — with --report, format report output like Kraken 1's kraken-mpa-report. throwback era 🎀
• --report-zero-counts — with --report, report counts for ALL taxa, even if counts are zero. nobody gets left out of this report, not even the zeros 💜
• --memory-mapping — avoids loading database into RAM. for when your RAM is going through it and you need to be gentle 🌈
• --paired — the filenames you provided have paired-end reads. tell her that, she's not a mind reader.
• --use-names — print scientific names instead of just taxids. so you get actual words instead of mysterious numbers ✨
• --gzip-compressed — input files are compressed with gzip.
• --bzip2-compressed — input files are compressed with bzip2.
• --help — print this message. she's helping 🫶
• --version — print version information.

ngl, important one: if none of the *-compressed flags are specified, and the filename you gave is a regular file, automatic format detection is attempted. she'll try to figure it out herself. queen behavior, but y'know. she's guessing.

🌸 AUTHOR 🌸

this manpage was written by Andreas Tille for the Debian distribution, and can be used for any other usage of the program. thank you Andreas, we appreciate you 💖

and that's the whole page bestie, we ate and left no crumbs 🍓 kraken2 2.0.7~beta, dated March 2019 — yes it's an old beta and she's still iconic, cry about it 😭💅