NAME

coords2gff.pl - convert mummer coords files to gff3 format

SYNOPSIS

# store results in OUTPUT.gff3
perl coords2gff.pl [OPTIONS] <MUMMER_ALIGNMENT.coords> <OUTPUT.gff3>

# print results to standard output
perl coords2gff.pl [OPTIONS] <MUMMER_ALIGNMENT.coords>
# or
perl coords2gff.pl [OPTIONS] <MUMMER_ALIGNMENT.coords> -

DESCRIPTION

This script converts mummer output in coords files to gff3 formatted output.

OPTIONS

Alternative option names are separated by "|".

--switch-query-reference|switch|s: Take the query (2nd sequence in the alignment) as reference and the reference (1st sequence in the alignment) as query. Adjust coordinates accordingly.
--help|h|?: Complete help.

AUTHOR

jw bargsten, <joachim.bargsten at wur.nl>

To install Bio::Gonzales, copy and paste the appropriate command in to your terminal.

cpanm

cpanm Bio::Gonzales

CPAN shell

perl -MCPAN -e shell
install Bio::Gonzales

For more information on module installation, please visit the detailed CPAN module installation guide.

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NAME

SYNOPSIS

DESCRIPTION

OPTIONS

SEE ALSO

AUTHOR

Module Install Instructions