bowtie-build - Online in the Cloud

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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