bowtie2-build-l - building a colorspace index for bowtie2
bowtie2-build-l [
options]
* <reference_in>
<bt2_index_base>
- Bowtie 2 version 2.5.0 by Ben Langmead ([email protected],
www.cs.jhu.edu/~langmea)
- reference_in
- comma-separated list of files with ref sequences
- bt2_index_base
- write bt2l data to files with this dir/basename
*** Bowtie 2 indexes will work with Bowtie v1.2.3 and later. ***
-f reference files are Fasta (default)
- -c
- reference sequences given on cmd line (as
<reference_in>)
-
-a/--noauto
- disable automatic -p/--bmax/--dcv
memory-fitting
-
-p/--packed
- use packed strings internally; slower, less memory
-
--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 index files
-
-3/--justref
- just build .3/.4 index files
-
-o/--offrate <int>
- SA is sampled every 2^<int> BWT chars (default:
5)
-
-t/--ftabchars <int>
- # of chars consumed in initial lookup (default: 10)
-
--threads <int>
- # of threads
-
--seed <int>
- seed for random number generator
-
-q/--quiet
- verbose output (for debugging)
-
--h/--help
- print this message and quit
- --version
- print version information and quit