This is the command bowtie2-build-s that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
bowtie2-build-s - building a colorspace index for bowtie2
SYNOPSIS
bowtie2-build-s [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 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)
-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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