CENTRIFUGE-BUILD(1)

💖 CENTRIFUGE-BUILD(1) 💖

okay bestie, welcome to the centrifuge-build page — User Commands energy, and yes this is the one that builds an index on all complete bacterial and viral genomes. iconic behavior fr fr. 🦠✨

🌸 NAME 🌸

centrifuge-build — building index on all complete bacterial and viral genomes

✨ SYNOPSIS ✨

centrifuge-build [options]* --conversion-table <table file> --taxonomy-tree <taxonomy tree file> <reference_in> <cf_index_base>

🎀 DESCRIPTION 🎀

Centrifuge version 1.0.3-beta by Daehwan Kim (infphilo@gmail.com, http://www.ccb.jhu.edu/people/infphilo) — no cap, that's the whole vibe of this tool, and we're obsessed. 💅

• reference_in — a comma-separated list of files with ref sequences. like, comma. separated. don't forget, bestie 🙈
• centrifuge_index_base — write cf data to files with this dir/basename

🔥 OPTIONS 🔥

• -c — reference sequences given on cmd line (as <reference_in>)
• --large-index — force generated index to be 'large', even if ref has fewer than 4 billion nucleotides. main character energy, it doesn't care that it doesn't need to be big 💀
• -a/--noauto — disable automatic -p/--bmax/--dcv memory-fitting
• --bmax <int> — max bucket sz for blockwise suffix-array builder
• --bmaxdivn <int> — max bucket sz as divisor of ref len (default: 4)
• --dcv <int> — diff-cover period for blockwise (default: 1024)
• --nodc — disable diff-cover (algorithm becomes quadratic). ⚠️ yeah she gets quadratic, so be careful, that's not a cute look on a big ref
• -r/--noref — don't build .3/.4.bt2 (packed reference) portion
• -3/--justref — just build .3/.4.bt2 (packed reference) portion
• -o/--offrate <int> — SA is sampled every 2^offRate BWT chars (default: 5)
• -t/--ftabchars <int> — # of chars consumed in initial lookup (default: 10)
• --conversion-table <file name> — a table that converts any id to a taxonomy id
• --taxonomy-tree <file name> — taxonomy tree
• --name-table <file name> — names corresponding to taxonomic IDs
• --size-table <file name> — table of contig (or genome) sizes
• --seed <int> — seed for random number generator
• -q/--quiet — verbose output (for debugging)
• -p/--threads <int> — number of alignment threads to launch (1)
• --kmer-count <int> — k size for counting the number of distinct k-mer
• -h/--help — print detailed description of tool and its options
• --usage — print this usage message
• --version — print version information and quit

👑 AUTHOR 👑

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. 🫶

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

centrifuge-build 1.0.3 💖 October 2021 — written with love, running on pure vibes and also actual Unix. bye bestie, go build that index 💅✨