SYNOPSIS
bowtie2-build [,options/],* <reference_in> <bt2_index_base>/DESCRIPTION
- Bowtie 2 version 2.2.9 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 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 <reference_in>)
- --large-index
- force generated index to be 'large', even if ref has fewer than 4 billion nucleotides
- -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 detailed description of tool and its options
- --usage
- print this usage message
- --version
-
print version information and quit