debian man page for bowtie2-build

BOWTIE2-BUILD(1)						   User Commands						  BOWTIE2-BUILD(1)

NAME
       bowtie2-build - building a colorspace index for bowtie2

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

DESCRIPTION
       Bowtie 2 version 2.0.0-beta6 by Ben Langmead (blangmea@jhsph.edu)

       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 <seq_in>)

       -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.bt2 (packed reference) portion

       -3/--justref
	      just build .3/.4.bt2 (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)

       --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  lxcsid Fri Jun  1 20:11:23 UTC 2012 Compiler: gcc version 4.7.0 (Debian 4.7.0-8) Options: -O3 -m64 -msse2 -funroll-loops
       -g3 Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}

bowtie2-build version 2.0.0-beta6				     June 2012							  BOWTIE2-BUILD(1)