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bowtie2-build - wrapper for bowtie2-build-*


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


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
use the debug binary; slower, assertions enabled
log the issued command
disable automatic -p/--bmax/--dcv memory-fitting
use packed strings internally; slower, less memory
max bucket sz for blockwise suffix-array builder
max bucket sz as divisor of ref len (default: 4)
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
SA is sampled every 2^<int> BWT chars (default: 5)
# of chars consumed in initial lookup (default: 10)
# of threads
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
March 2021 bowtie2-build 2.4.2