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PROGRAM:

NAME


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

SYNOPSIS


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

DESCRIPTION


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

reference_in
comma-separated list of files with ref sequences

bt2_index_base
write bt2l 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)

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

-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)

--seed <int>
seed for random number generator

-q/--quiet
verbose output (for debugging)

-h/--help
print detailed description of tool and its options

--usage
print this usage message

--version
print version information and quit

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