The GFF3toolkit: QC and merge pipeline for genome annotation

Abstract

The GFF3toolkit (https://github.com/NAL-i5K/GFF3toolkit) supported by the i5k Workspace@NAL provides a suite of tools to handle gene annotations in GFF3 format from arthropod genome projects and their research communities. To improve GFF3 formatting of gene annotations, a quality control and merge procedure is proposed along with the GFF3toolkit. In particular, the toolkit provides functions to sort a GFF3 file, detect GFF3 format errors, merge two GFF3 files, and generate biological sequences from a GFF3 file. This chapter explains when and how to use the provided tools to obtain nonredundant arthropod gene sets in high quality.