Indexing genomes for bowtie

general

bowtie-build [options] <reference_in> <index_basename>

e.g. bowtie-build -f build37.fa build37
[-f : the reference file is in fasta format (see below)]

info

Usage: bowtie-build [options]* <reference_in> <ebwt_outfile_base>

   reference_in            comma-separated list of files with ref sequences
   ebwt_outfile_base       write Ebwt data to files with this dir/basename

Options:

   -f                      reference files are Fasta (default)
   -c                      reference sequences given on cmd line (as <seq_in>)
   -C/--color              build a colorspace index
   -a/--noauto             disable automatic -p/--bmax/--dcv memory-fitting
   -p/--packed             use packed strings internally; slower, uses less mem
   -B                      build both letter- and colorspace indexes
   --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.ebwt (packed reference) portion
   -3/--justref            just build .3/.4.ebwt (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)
   --ntoa                  convert Ns in reference to As
   --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