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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>)
--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)
--threads <int>
# of threads
--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, 05 Sep 2019 17:49:44 +0200 Compiler: gcc version 9.2.1 20190827 Options: -O3 -Wl,--hash-style=both -DWITH_TBB -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 -std=c++03 -Wl,-z,relro -Wl,-z,now Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}

September 2019 bowtie-build version 1.2.3