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