NAME
bowtie2-build - wrapper for bowtie2-build-*
SYNOPSIS
bowtie2-build [options]* <reference_in> <bt2_index_base>
DESCRIPTION
- 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
- -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