centrifuge-build - building index on all complete bacterial and viral genomes

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

centrifuge-build 1.0.3                            October 2021                               CENTRIFUGE-BUILD(1)

       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

       centrifuge-build - building index on all complete bacterial and viral genomes

-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

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