Provided by: bowtie2_2.3.4.1-1_amd64 bug


       bowtie2-build-l - building a colorspace index for bowtie2


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


       Bowtie 2 version by Ben Langmead (,

              comma-separated list of files with ref sequences

              write bt2l data to files with this dir/basename

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


       -f reference files are Fasta (default)

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

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

              use packed strings internally; slower, less memory

       --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 index files

              just build .3/.4 index files

       -o/--offrate <int>
              SA is sampled every 2^<int> BWT chars (default: 5)

       -t/--ftabchars <int>
              # of chars consumed in initial lookup (default: 10)

       --threads <int>
              # of threads

       --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