Annotation and visualisation of parasite, fungi and arthropod genomes with Companion

Although sequencing genomes has become increasingly popular, there is still a bottleneck for the annotation of the resulting assemblies. Structural and functional annotation is still challenging as it includes finding the correct gene sequences, annotating other elements such as RNA and being able to submit those data to databases to share it with the community. We developed the Companion web server to allow non-experts to annotate their genome using a reference-based method, enabling them to analyse their results before submitting to public databases. In this update paper, we describe how we included novel methods for gene finding and made the server more efficient to annotate genomes of up to 1 GB in size. The reference set was increased to genomes from the fungi and arthropod kingdoms. We show that Companion outperforms existing comparable tools.