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}