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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



bowtie-build - building a colorspace index for bowtie


bowtie-build [options]* <reference_in> <ebwt_outfile_base>


comma-separated list of files with ref sequences

write Ebwt data to files with this dir/basename


-f reference files are Fasta (default)

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

force generated index to be 'large', even if ref has fewer than 4 billion

build a colorspace index

disable automatic -p/--bmax/--dcv memory-fitting

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)

don't build .3/.4.ebwt (packed reference) portion

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

verbose output (for debugging)

print detailed description of tool and its options

print this usage message

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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