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)

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

AUTHOR¶

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