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

       -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 Tue, 09 Dec 2025 23:19:38 +0000 Compiler: gcc version 15.2.0 Options:
       -O3     -Wl,--hash-style=both     -DPOPCNT_CAPABILITY     -Wdate-time    -D_FORTIFY_SOURCE=3    -g    -O2
       -Werror=implicit-function-declaration        -fno-omit-frame-pointer         -mno-omit-leaf-frame-pointer
       -ffile-prefix-map=.=.   -flto=auto  -ffat-lto-objects  -fstack-protector-strong  -fstack-clash-protection
       -Wformat -Werror=format-security -fcf-protection  -fdebug-prefix-map=.=/usr/src/bowtie-1.3.1-3build1   -g
       -O2     -fno-omit-frame-pointer     -mno-omit-leaf-frame-pointer     -ffile-prefix-map=.=.     -flto=auto
       -ffat-lto-objects  -fstack-protector-strong  -fstack-clash-protection  -Wformat   -Werror=format-security
       -fcf-protection  -fdebug-prefix-map=.=/usr/src/bowtie-1.3.1-3build1  -std=c++03  -Wl,-Bsymbolic-functions
       -Wl,--package-metadata={%22type%22:%22deb%22%2C%22os%22:%22ubuntu%22%2C%22name%22:%22bowtie%22%2C%22version%22:%221.3.1-3build1%22%2C%22architecture%22:%22amd64%22}
       -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now Sizeof {int, long, long long, void*, size_t, off_t}:
       {4, 8, 8, 8, 8, 8}

bowtie-build version 1.3.1                        December 2025                                  BOWTIE-BUILD(1)