Scroll to navigation



bowtie-build - 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
disable automatic -p/--bmax/--dcv memory-fitting
use packed strings internally; slower, uses less mem
max bucket sz for blockwise suffix-array builder
max bucket sz as divisor of ref len (default: 4)
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
SA is sampled every 2^offRate BWT chars (default: 5)
# of chars consumed in initial lookup (default: 10)
# of threads
convert Ns in reference to As
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 Tue, 14 Sep 2021 07:01:35 +0200 Compiler: gcc version 10.3.0 Options: -O3 -Wl,--hash-style=both -DPOPCNT_CAPABILITY -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=.=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 2021 bowtie-build version 1.3.1