Welcome to AGAT's documentation!

Another GTF/GFF Analysis Toolkit

The GTF/GFF formats are 9-column text formats used to describe and represent genomic features. The formats have quite evolved since 1997, and despite well-defined specifications existing nowadays they have a great flexibility allowing holding wide variety of information. This flexibility has a drawback aspect, there is an incredible amount of flavor of the formats: GFF / GFF1 / GFF2 / GFF2.5 / GFF3 / GTF / GTF2 / GTF2.1 / GTF2.2 / GTF2.5 / GTF3

It's often hard to understand and differentiate all GFF/GTF formats/flavors. Many tools using GTF/GFF formats fails due to specific expectations. AGAT is a suite of tools able to deal with any GTF/GFF formats and perform most of the possible tasks you would need.

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Contents

List of tools

Indices and tables