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
- -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, 25 Jan 2024 12:27:31 +0100 Compiler: gcc version 13.2.0 Options: -O3 -Wl,--hash-style=both -DPOPCNT_CAPABILITY -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=.=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -ffile-prefix-map=.=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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}