bowtie-build - building a colorspace index for bowtie

       reference_in
              comma-separated list of files with ref sequences

       ebwt_outfile_base
              write Ebwt data to files with this dir/basename

       bowtie-build - building a colorspace index for bowtie

-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 Thu, 25 Jan 2024 12:27:31 +0100 Compiler: gcc version 13.2.0 Options:
       -O3-Wl,--hash-style=both     -DPOPCNT_CAPABILITY-Wdate-time-D_FORTIFY_SOURCE=3-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-1.3.1-3  -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-1.3.1-3 -std=c++03
       -Wl,-Bsymbolic-functions -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                        January 2024                                   BOWTIE-BUILD(1)

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