coords2gff.pl - convert mummer coords files to gff3 format
# 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> -
This script converts mummer output in coords files to gff3 formatted output.
Alternative option names are separated by "|".
Take the query (2nd sequence in the alignment) as reference and the reference (1st sequence in the alignment) as query. Adjust coordinates accordingly.
Complete help.
Bio::FeatureIO, Bio::SeqFeature::Generic
jw bargsten, <joachim.bargsten at wur.nl>
<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.