centrifuge-build1

Building index on all complete bacterial and viral genomes

Usage

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

Overview

Centrifuge version 1.0.3-beta by Daehwan Kim ([email protected], http://www.ccb.jhu.edu/people/infphilo)

`reference_in`	comma-separated list of files with ref sequences
`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

-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)

`-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

Releases

4 releases since Debian 10 (Buster); the text changed 1 time.

--bmax since Debian 12 (Bookworm); --bmaxdivn since Debian 12 (Bookworm); --dcv since Debian 12 (Bookworm); --kmer-count since Debian 12 (Bookworm); --large-index since Debian 12 (Bookworm); --name-table since Debian 12 (Bookworm); --nodc since Debian 12 (Bookworm); --seed since Debian 12 (Bookworm); --size-table since Debian 12 (Bookworm); --taxonomy-tree since Debian 12 (Bookworm); --usage since Debian 12 (Bookworm); --version since Debian 12 (Bookworm); -c since Debian 12 (Bookworm).