Provided by: bowtie2_2.1.0-2_amd64 bug


       bowtie2-build - building a colorspace index for bowtie2


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


       No  input  sequence  or  sequence  file specified!  Bowtie 2 version 2.1.0 by Ben Langmead

              comma-separated list of files with ref sequences

              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>)

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

              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)

              don't build .3/.4.bt2 (packed reference) portion

              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

              verbose output (for debugging)

              print detailed description of tool and its options

              print this usage message

              print version information and quit