NAME

       bowtie-build - building a colorspace index for bowtie

SYNOPSIS

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

DESCRIPTION

       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>)

       --large-index
              force  generated  index  to  be  'large',  even  if  ref  has  fewer than 4 billion
              nucleotides

       -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

       --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)

       --threads <int>
              # of threads

       --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

       64-bit Built on Debian-reproducible Wed, 31 Jan 2018 14:04:41 +0100 Compiler: gcc  version
       7.3.0  Options:  -O3   -Wl,--hash-style=both -DWITH_TBB -Wdate-time -D_FORTIFY_SOURCE=2 -g
       -O2 -fdebug-prefix-map=.=. -fstack-protector-strong -Wformat  -Werror=format-security   -g
       -O2   -fdebug-prefix-map=.=.   -fstack-protector-strong  -Wformat  -Werror=format-security
       -std=c++03 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now Sizeof {int, long, long  long,
       void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}