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.