NAME

       bowtie2-build - building a colorspace index for bowtie2

SYNOPSIS

       bowtie2-build [options]* <reference_in> <bt2_index_base>

DESCRIPTION

       No  input  sequence  or  sequence  file specified!  Bowtie 2 version 2.1.0 by Ben Langmead
       (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)

       reference_in
              comma-separated list of files with ref sequences

       bt2_index_base
              write .bt2 data to files with this dir/basename

       *** Bowtie 2 indexes work only with v2 (not v1).  Likewise for v1 indexes. *** Options:

       -f     reference files are Fasta (default)

       -c     reference sequences given on cmd line (as <seq_in>)

       -a/--noauto
              disable automatic -p/--bmax/--dcv memory-fitting

       -p/--packed
              use packed strings internally; slower, uses less mem

       --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)

       --seed <int>
              seed for random number generator

       -q/--quiet
              verbose output (for debugging)

       -h/--help
              print detailed description of tool and its options

       --usage
              print this usage message

       --version
              print version information and quit