debian man page for bowtie-build

BOWTIE-BUILD(1) 						   User Commands						   BOWTIE-BUILD(1)

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>)

       -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

       -B     build both letter- and colorspace indexes

       --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)

       --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 wr-linux02 Tue Apr 24 11:36:57 UTC 2012 Compiler: gcc version 4.6.3 (Debian 4.6.3-4) Options: -O3   -Wl,--hash-style=both
       -D_FORTIFY_SOURCE=2  -g	-O2  -fstack-protector	--param=ssp-buffer-size=4  -Wformat  -Wformat-security	-Werror=format-security   -g   -O2
       -fstack-protector  --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security	-Wl,-z,relro Sizeof {int, long, long long,
       void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}

bowtie-build version 0.12.7					    April 2012							   BOWTIE-BUILD(1)