bowtie-build(1) building a colorspace index for bowtie


bowtie-build [,options/],* <reference_in> <ebwt_outfile_base>/


comma-separated list of files with ref sequences
write Ebwt data to files with this dir/basename


reference files are Fasta (default)
reference sequences given on cmd line (as <seq_in>)
force generated index to be 'large', even if ref has fewer than 4 billion nucleotides
build a colorspace index
disable automatic -p/--bmax/--dcv memory-fitting
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)
disable diff-cover (algorithm becomes quadratic)
don't build .3/.4.ebwt (packed reference) portion
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)
convert Ns in reference to As
--seed <int>
seed for random number generator
verbose output (for debugging)
print detailed description of tool and its options
print this usage message
print version information and quit

64-bit Built on Debian-reproducible Wed, 25 May 2016 22:25:27 +0000 Compiler: gcc version 5.3.1 20160519 Options: -O3 -Wl,--hash-style=both -Wdate-time -D_FORTIFY_SOURCE=,2/ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=,format-security/ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=,format-security/ -fPIE -pie -Wl,-z,relro -Wl,-z,now Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}