bowtie-build - building a colorspace index for bowtie
bowtie-build [options]* <reference_in>
<ebwt_outfile_base>
- -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 Tue, 13 Oct 2020 13:16:39
+0200 Compiler: gcc version 10.2.0 Options: -O3
-Wl,--hash-style=both -DPOPCNT_CAPABILITY -Wdate-time
-D_FORTIFY_SOURCE=2 -g -O2
-fdebug-prefix-map=.=. -fstack-protector-strong
-Wformat -Werror=format-security -g -O2
-fdebug-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}