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BOWTIE-BUILD

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>)

−−large−index

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

−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

−−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 Debian−reproducible Thu, 08 Jun 2017 15:24:17 +0200 Compiler: gcc version 6.3.0 20170519 Options: −O3 −Wl,−−hash−style=both −DWITH_TBB −DNO_SPINLOCK −DWITH_QUEUELOCK=1 −Wdate−time −D_FORTIFY_SOURCE=2 −g −O2 −fdebug−prefix−map=.=. −fstack−protector−strong −Wformat −Werror=format−security −g −O2 −fdebug−prefix−map=.=. −fstack−protector−strong −Wformat −Werror=format−security −Wl,−Bsymbolic−functions −Wl,−z,relro −Wl,−z,now Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}

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