bowtie2-build-s1
Building a colorspace index for bowtie2
Usage
bowtie2-build-s [options]
*
<reference_in>
<bt2_index_base>
Overview
- Bowtie 2 version 2.5.4 by Ben Langmead ([email protected], www.cs.jhu.edu/~langmea)
- 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 will work with Bowtie v1.2.3 and later. ***
Options
-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
History
- Debian 13 (Trixie): the text shown here
- Debian 12 (Bookworm)
- Debian 11 (Bullseye)
- Debian 10 (Buster)
- Debian 9 (Stretch)
- Debian 8 (Jessie)
--threads since Debian 9 (Stretch).
--usage until Debian 11 (Bullseye);
-f until Debian 8 (Jessie).