KRAKEN2-BUILD(1)

💖 KRAKEN2-BUILD — the manual page, bestie edition 💖

okay so. this is kraken2-build, manual section 1, and it's literally the tool for assigning taxonomic labels to short DNA sequences. it's giving "i classify your reads and i do it gorgeously". let's get into it 🦋

✨ SYNOPSIS ✨

kraken2-build [task option] [options]

yeah that's it. one task, a lil pile of options, we move. 💅

🌸 DESCRIPTION 🌸

🎀 Task options (exactly one must be selected) 🎀

bestie listen. exactly one. not two, not zero. pick one task option or the whole thing gets awkward.

• --download-taxonomy — pulls down the NCBI taxonomic information. the family tree data, basically. 🌳
• --download-library TYPE — grabs a partial library. TYPE has to be one of these, no substitutions, no vibes-based guessing:
  • "archaea"
  • "bacteria"
  • "plasmid"
  • "viral"
  • "human"
  • "fungi"
  • "plant"
  • "protozoa"
  • "nr"
  • "nt"
  • "env_nr"
  • "env_nt"
  • "UniVec"
  • "UniVec_Core"
• --special TYPE — downloads and builds a special database in one go. TYPE is one of:
  • "greengenes"
  • "silva"
  • "rdp"
• --add-to-library FILE — drops FILE into your library. one file at a time, queen. 🍓
• --build — makes the DB from your library. ⚠️ requires that you already downloaded the taxonomy and have at least one file sitting in the library. it will not manifest sequences out of thin air, no cap.
• --clean — sweeps the unneeded files out of a built database. self-care. 🧹✨
• --standard — downloads and builds the default database. the "just give me the standard one" button. 👑
• --help — prints this message. 🫶
• --version — prints version info.

💅 OPTIONS 💅

• --db NAME — the Kraken 2 DB / library name. mandatory unless you're doing --help or --version. so like, always, basically.
• --threads # — how many threads you want. default is 1. give it more if your machine can handle the main character energy. 🔥
• --kmer-len NUM — k-mer length in bp/aa. build task only. default is 35 nt, 15 aa.
• --minimizer-len NUM — minimizer length in bp/aa. build task only. default is 31 nt, 15 aa.
• --minimizer-spaces NUM — how many characters in the minimizer get ignored during comparisons. build task only. default is 6 nt, 0 aa.
• --protein — builds a protein database, for translated search. 🧬
• --no-masking — use this alongside --standard, --download-library, or --add-to-library to skip masking low-complexity sequences before building. masking needs dustmasker or segmasker installed in PATH, and honestly some users just don't have that, so here's your escape hatch. 🚪
• --max-db-size NUM — the max number of bytes for the Kraken 2 hash table. if the estimator decides more would normally be needed, the reference library gets downsampled to fit. used with --build, --standard, or --special. ✂️

🌈 AUTHOR 🌈

this manpage was written by Andreas Tille for the Debian distribution, and it can be used for any other usage of the program too. generous icon behavior honestly. 💜

and that's the whole page, bestie!! this was kraken2-build version 2.0.7~beta, dated March 2019 — the manpage came from the User Commands section of the Debian man pages, and yes, the date really is 2019. vintage. retro. still slaying. 🎀✨🦋