KRAKEN(1)

👑 KRAKEN — like, the manual page, bestie 💅

okay so welcome to kraken(1), a User Commands situation, and honestly? she's iconic. buckle up, we're assigning taxonomic labels to short DNA sequences and we're gonna have a time. 🧬✨

🌸 NAME 🌸

kraken — the girl who assigns taxonomic labels to short DNA sequences. that's the whole job description, no notes. 🦋

💖 SYNOPSIS 💖

kraken [options] <filename(s)>

like, you give her options and filenames, and she works. periodt. 👑

✨ OPTIONS ✨

okay here's the menu, and yes you're gonna read all of it, i love you but i'm not summarising 💜

• --db NAME — the Name for your Kraken DB. default? none. so like, set this or perish. 🙈
• --threads NUM — Number of threads. default is 1, so if you're sitting there watching her crawl, that's on you bestie, crank it. 🔥
• --fasta-input — Input is FASTA format. classic. 🎀
• --fastq-input — Input is FASTQ format. the other classic. 🍓
• --gzip-compressed — Input is gzip compressed. zipped up and still slaying. ✨
• --bzip2-compressed — Input is bzip2 compressed. different compression, same energy. 🌈
• --quick — Quick operation — she uses the first hit or hits. speed over thoroughness, main character behaviour ngl. ⭐
• --min-hits NUM — in quick op., this is the number of hits req'd for classification. NOTE: this is ignored if --quick is not specified. so like, don't set it and expect vibes, because nothing will happen. 💀
• --unclassified-out FILENAME — Print unclassified sequences to filename. we're not losing them, they just go somewhere else. 🫶
• --classified-out FILENAME — Print classified sequences to filename. same deal, opposite direction. 🎀
• --output FILENAME — Print output to filename. default is stdout (so, your terminal, where she lives). and btw, a - will suppress normal output. yes, -. literally that one dash. 😭
• --only-classified-output — Print no Kraken output for unclassified sequences. they simply do not get a moment. 💅
• --preload — Loads the DB into memory before classification. impatient queen behaviour, valid. 🔥
• --paired — The two filenames you provided are paired-end reads. two files, one destiny. 💞
• --check-names — Ensure each pair of reads have names that agree with each other. and listen: this one is ignored if --paired is not specified, so don't be out here using it solo. 👑
• --help — Print this message. hi, you found it. 🌸
• --version — Print version information. the receipts. 🧾

quick lil PSA before you go: If none of the *-input or *-compressed flags are specified, and the file is a regular file, automatic format detection is attempted. so she'll sniff it out herself. she's that girl. 🦋

and that's the whole page, bestie!! this was kraken 0.10.5~beta, dated September 2015 — yeah, she's a lil vintage but she ate and left no crumbs. mwah, go classify something 💋💖✨