NAME

       bowtie2-build - wrapper for bowtie2-build-*

SYNOPSIS

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

DESCRIPTION

       Bowtie 2 version 2.3.5.1 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)

       reference_in
              comma-separated list of files with ref sequences

       bt2_index_base
              write bt2 data to files with this dir/basename

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

OPTIONS

       -f reference files are Fasta (default)

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

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

       --debug
              use the debug binary; slower, assertions enabled

       --sanitized
              use sanitized binary; slower, uses ASan and/or UBSan

       --verbose
              log the issued command

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

       -p/--packed
              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)

       -r/--noref
              don't build .3/.4 index files

       -3/--justref
              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

       -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