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

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

NAME

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

SYNOPSIS

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

DESCRIPTION

Bowtie 2 version 2.3.3.1 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)
--threads <int>
# of threads
--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
October 2017 bowtie2-build-l 2.3.3.1