bowtie2-build1
Wrapper for bowtie2-build-*
Usage
bowtie2-build [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>)
-
--large-index -
force generated index to be 'large', even if ref has fewer than 4 billion nucleotides
-
--debug -
use the debug binary; slower, assertions enabled
-
--verbose -
log the issued command
|
disable automatic |
|---|---|
|
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)
|
don't build .3/.4 index files |
|---|---|
|
just build .3/.4 index files |
|
SA is sampled every 2^<int> BWT chars (default: 5) |
|
# of chars consumed in initial lookup (default: 10) |
-
--threads <int> -
# of threads
-
--seed <int> -
seed for random number generator
|
verbose output (for debugging) |
|---|---|
|
print this message and quit |
-
--version -
print version information and quit
Releases
7 releases since Debian 7 (Wheezy); the text changed 6 times.
--bmax since Debian 9 (Stretch);
--bmaxdivn since Debian 9 (Stretch);
--dcv since Debian 9 (Stretch);
--debug since Debian 10 (Buster);
--large-index since Debian 9 (Stretch);
--nodc since Debian 9 (Stretch);
--seed since Debian 9 (Stretch);
--threads since Debian 9 (Stretch);
--verbose since Debian 10 (Buster);
--version since Debian 9 (Stretch);
-c since Debian 9 (Stretch).
--sanitized until Debian 10 (Buster);
--usage until Debian 11 (Bullseye);
-f until Debian 7 (Wheezy).