bowtie-build - building a colorspace index for bowtie
bowtie-build [
options]
* <reference_in>
<ebwt_outfile_base>
- reference_in
- comma-separated list of files with ref sequences
- ebwt_outfile_base
- write Ebwt data to files with this dir/basename
- -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 Mon, 19 Sep 2022 02:49:13 +0000 Compiler:
gcc version 12.2.0 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}