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BOWTIE2-BUILD-S(1) User Commands BOWTIE2-BUILD-S(1)

NAME

bowtie2-build-s - building a colorspace index for bowtie2

SYNOPSIS

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

DESCRIPTION

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. ***

OPTIONS

-f reference files are Fasta (default)

reference sequences given on cmd line (as <reference_in>)
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
-3/--justref
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
September 2021 bowtie2-build-s 2.4.4