Blog:Review of the GFF and GTF formats (GFF / GFF1 / GFF2 / GFF2.5 / GFF3 / GTF / GTF2 / GTF2.1 / GTF2.2 / ...)

Question

[Juke34]

I have always been using GTF and GFF files and discovered peculiarities as we go along. After all this years I realised that some information related to those formats sounded still mystic to me. Despite the different information available in many "official" places, some sides of the formats and especially the origin and the evolution of the differents flavors was still unclear. To disentangle everything I decided to make a comprehensive review of those formats. Even if this review has not answered all my questions that has been really informative and allowed me to (re-)discovered many useful information.

I guess this work can be useful for many of us, so here is the place to have a look at it:

https://nbisweden.github.io/AGAT/gxf/
or
https://agat.readthedocs.io/en/latest/gxf.html
or
https://github.com/NBISweden/GAAS/blob/master/annotation/knowledge/gxf.md

Timeline of the different formats:

Answer 1

[Istvan Albert]

pretty mindboggling.

I personally blame tophat as the tool that resurrected the dead GTF format. GFF seemed to have a great uptake and seemed to squeeze out GTF. Then tophat (version 1) was released and it required a GTF format. It is hard to convey how influential tophat was just a few years ago. By today tophat 1 is obsolete, but the resurrected format lives on.