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)
- --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 anx191 Tue Feb 3 01:56:23 UTC 2015 Compiler: gcc version 4.9.2
(Debian 4.9.2-10) Options:
-O3 -Wl,--hash-style=both
-DPOPCNT_CAPABILITY -D_FORTIFY_SOURCE=
2 -g
-O2 -fstack-protector-strong -Wformat
-Werror=
format-security -g -O2
-fstack-protector-strong -Wformat
-Werror=
format-security -Wl,-z,relro Sizeof {int, long,
long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}