bowtie2-build(1) wrapper for bowtie2-build-*


bowtie2-build [,options/],* <reference_in> <bt2_index_base>/


Bowtie 2 version 2.2.9 by Ben Langmead ([email protected],
comma-separated list of files with ref sequences
write bt2 data to files with this dir/basename

*** Bowtie 2 indexes work only with v2 (not v1). Likewise for v1 indexes. ***


-f reference files are Fasta (default)
reference sequences given on cmd line (as <reference_in>)
force generated index to be 'large', even if ref has fewer than 4 billion nucleotides
disable automatic -p/--bmax/--dcv memory-fitting
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)
disable diff-cover (algorithm becomes quadratic)
don't build .3/.4 index files
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
verbose output (for debugging)
print detailed description of tool and its options
print this usage message
print version information and quit