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)
