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