bowtie-build − building a colorspace index for bowtie
bowtie-build [options]* <reference_in> <ebwt_outfile_base>
reference_in
comma−separated list of files with ref sequences
ebwt_outfile_base
write Ebwt data to files with this dir/basename
−f |
reference files are Fasta (default) |
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−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}