.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.48.1.
.TH CENTRIFUGE-BUILD "1" "October 2021" "centrifuge-build 1.0.3" "User Commands"
.SH NAME
centrifuge-build \- building index on all complete bacterial and viral genomes
.SH SYNOPSIS
.B centrifuge-build
[\fI\,options\/\fR]\fI\,* --conversion-table <table file> --taxonomy-tree <taxonomy tree file> <reference_in> <cf_index_base>\/\fR
.SH DESCRIPTION
Centrifuge version 1.0.3\-beta by Daehwan Kim (infphilo@gmail.com, http://www.ccb.jhu.edu/people/infphilo)
.TP
reference_in
comma\-separated list of files with ref sequences
.TP
centrifuge_index_base
write cf data to files with this dir/basename
.SH OPTIONS
.TP
\fB\-c\fR
reference sequences given on cmd line (as
<reference_in>)
.TP
\fB\-\-large\-index\fR
force generated index to be 'large', even if ref
has fewer than 4 billion nucleotides
.TP
\fB\-a\fR/\-\-noauto
disable automatic \fB\-p\fR/\-\-bmax/\-\-dcv memory\-fitting
.TP
\fB\-\-bmax\fR <int>
max bucket sz for blockwise suffix\-array builder
.TP
\fB\-\-bmaxdivn\fR <int>
max bucket sz as divisor of ref len (default: 4)
.TP
\fB\-\-dcv\fR <int>
diff\-cover period for blockwise (default: 1024)
.TP
\fB\-\-nodc\fR
disable diff\-cover (algorithm becomes quadratic)
.TP
\fB\-r\fR/\-\-noref
don't build .3/.4.bt2 (packed reference) portion
.TP
\fB\-3\fR/\-\-justref
just build .3/.4.bt2 (packed reference) portion
.TP
\fB\-o\fR/\-\-offrate <int>
SA is sampled every 2^offRate BWT chars (default: 5)
.TP
\fB\-t\fR/\-\-ftabchars <int>
# of chars consumed in initial lookup (default: 10)
.TP
\fB\-\-conversion\-table\fR <file name>
a table that converts any id to a taxonomy id
.TP
\fB\-\-taxonomy\-tree\fR
<file name>  taxonomy tree
.TP
\fB\-\-name\-table\fR
<file name>  names corresponding to taxonomic IDs
.TP
\fB\-\-size\-table\fR
<file name>  table of contig (or genome) sizes
.TP
\fB\-\-seed\fR <int>
seed for random number generator
.TP
\fB\-q\fR/\-\-quiet
verbose output (for debugging)
.TP
\fB\-p\fR/\-\-threads <int>
number of alignment threads to launch (1)
.TP
\fB\-\-kmer\-count\fR <int>
k size for counting the number of distinct k\-mer
.TP
\fB\-h\fR/\-\-help
print detailed description of tool and its options
.TP
\fB\-\-usage\fR
print this usage message
.TP
\fB\-\-version\fR
print version information and quit
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.