NAME¶
bowtie2-build - building a colorspace index for bowtie2
SYNOPSIS¶
bowtie2-build [
options]
* <reference_in>
<bt2_index_base>
DESCRIPTION¶
Bowtie 2 version 2.0.0-beta6 by Ben Langmead (blangmea@jhsph.edu)
- reference_in
- comma-separated list of files with ref sequences
- bt2_index_base
- write .bt2 data to files with this dir/basename
*** Bowtie 2 indexes work only with v2 (not v1). Likewise for v1 indexes. ***
Options:
- -f
- reference files are Fasta (default)
- -c
- reference sequences given on cmd line (as
<seq_in>)
- -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.bt2 (packed reference) portion
- -3/--justref
- just build .3/.4.bt2 (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)
- --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 lxcsid Fri Jun 1 20:11:23 UTC 2012 Compiler: gcc version 4.7.0
(Debian 4.7.0-8) Options:
-O3 -m64 -msse2
-funroll-loops -g3 Sizeof {int, long, long long, void*, size_t,
off_t}: {4, 8, 8, 8, 8, 8}