This is the command bowtie-build 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
bowtie-build - building a colorspace index for bowtie
SYNOPSIS
bowtie-build [options]* <reference_in> <ebwt_outfile_base>
DESCRIPTION
reference_in
comma-separated list of files with ref sequences
ebwt_outfile_base
write Ebwt data to files with this dir/basename
OPTIONS
-f reference files are Fasta (default)
-c reference sequences given on cmd line (as <seq_in>)
--large-index
force generated index to be 'large', even if ref has fewer than 4 billion
nucleotides
-C/--color
build a colorspace index
-a/--noauto
disable automatic -p/--bmax/--dcv memory-fitting
-p/--packed
use packed strings internally; slower, uses less mem
--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.ebwt (packed reference) portion
-3/--justref
just build .3/.4.ebwt (packed reference) portion
-o/--offrate <int>
SA is sampled every 2^offRate BWT chars (default: 5)
-t/--ftabchars <int>
# of chars consumed in initial lookup (default: 10)
--ntoa convert Ns in reference to As
--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
64-bit Built on lgw01-11 Thu Nov 26 11:11:03 UTC 2015 Compiler: gcc version 5.2.1 20151123
(Ubuntu 5.2.1-25ubuntu1) Options: -O3 -Wl,--hash-style=both -D_FORTIFY_SOURCE=2 -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fstack-protector-strong
-Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro Sizeof {int, long,
long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}
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