KRAKEN-BUILD(1)

💖 KRAKEN-BUILD(1) 💖

okay so bestie, welcome to kraken-build — it's a User Commands page and honestly? it's giving taxonomy girlboss. we're assigning taxonomic labels to short DNA sequences and we're gonna have a time. 🦋

✨ NAME ✨

kraken-build — assigning taxonomic labels to short DNA sequences 💅

🌸 SYNOPSIS 🌸

kraken-build [task option] [options]

🎀 DESCRIPTION 🎀

💫 Task options (exactly one must be selected):

so like. you pick exactly one of these. not two. not zero. one. the way that the universe requires balance ✨

• --download-taxonomy — download NCBI taxonomic information 🧬
• --download-library TYPE — download a partial library, where TYPE is one of "bacteria", "plasmids", "viruses", "human" 🦠
• --add-to-library FILE — add FILE to the library 📁
• --build — create a DB from the library (this needs taxonomy already d/l'ed and at least one file sitting in the library, no cap) 🏗️
• --rebuild — create a DB from the library just like --build, except it removes existing non-library/taxonomy files before building 🧹
• --clean — remove unneeded files from a built database ✨
• --shrink NEW_CT — shrink an existing DB so it only has NEW_CT k-mers 🫧
• --standard — download and create the default database, iconic default behaviour 👑
• --upgrade — upgrade an existing older database to use scrambled minimizer ordering (peep the README for the deets) ⬆️
• --help — print this message 🙈
• --version — print version information ⭐

🔥 OPTIONS 🔥

• --db NAME — Kraken DB/library name. it's mandatory, bestie — except for --help / --version, those two get a free pass 💖
• --threads # — number of threads (def: 1) 🧵
• --new-db NAME — new Kraken DB name. shrink task only, and mandatory for the shrink task 👀
• --kmer-len NUM — k-mer length in bp. build/shrink tasks only (def: 31) 📏
• --minimizer-len NUM — minimizer length in bp. build/shrink tasks only (def: 15) 📐
• --jellyfish-hash-size STR — pass a specific hash size argument to jellyfish when building the database. build task only 🪼
• --max-db-size SIZE — shrink the DB before the full build, making sure the database and index together use <= SIZE gigabytes. build task only 📦
• --shrink-block-offset NUM — when shrinking, select the k-mer that is NUM positions from the end of a block of k-mers (default: 1) 🎯
• --work-on-disk — do most operations on disk instead of in RAM. heads up: this will slow down the build in most cases 🐌

fr fr, that last one is a tradeoff — on-disk means slower builds most of the time, but it's there if you need it 💀

and that's the whole page, bestie — you ate that 🫶

this was kraken-build 0.10.5~beta, dated September 2015, and it's been serving User Commands realness since. mwah 💋✨🎀