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bowtie2-build - wrapper for bowtie2-build-*


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


Bowtie 2 version 2.2.6 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)

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)

-c reference sequences given on cmd line (as <reference_in>)

force generated index to be 'large', even if ref has fewer than 4 billion

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)

--nodc 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)

--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

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