How to validate GFF3?
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8.7 years ago
mike.thon ▴ 30

What tools are available to validate a GFF3 format file? I tried the one recommended by the Sequence Ontology Project but it has been offline every time I try it. I also tried GenomeTools. It helps but it does not catch all of the errors.

gff • 4.6k views
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You may want to state what your purpose is (or the problem you are having) because different tools have slightly different definitions of what "valid" means.

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htseq has GFF_Reader method, which parse a GFF file.

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8.7 years ago
igor 13k

What about GFF tools?

http://www.raetschlab.org/suppl/gff-tools

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8.5 years ago
firestar ★ 1.6k

gff3validator from genometools? http://www.genometools.org/cgi-bin/gff3validator.cgi online web version and commandline tool.

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