Easy and reliable fungi genome annotation at the University of Glasgow - beta version.

Annotate your sequence!

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New Fungi instance.

We are currently seeking funding to develop a Companion instance for fungi at the University of Glasgow.
This current service is designed to work for closely related fungi species to the following fungi phyla: Aspergillus, Coccidioides, Cryptococcus, Phytophthora, Candida and Fusarium. A candida genomes takes about an hour to run. But fungi specific biology is not implemented. Therefore we consider this a beta server.
Please follow us twitter @AnnotationServer for the latest developments and updates.


Annotation of a new genome could be as easy as uploading your scaffold sequences (FASTA, EMBL, GenBank), choosing a reference (from our set of 25 species) and pushing a button!


The pipeline spans many aspects of new genome production, from pseudochromosome contiguation, structural and functional gene annotation over comparative analyses to visualization.

Standards compliant.

Annotation results are provided in validated GFF3 format for gene model and product annotations and GAF format for GO associations.


Annotation results are typically ready in a couple of hours. Submit multiple jobs at once and we will keep you up to date about the progress of your jobs.

High quality.

Data-generating components of the pipeline are built on time-tested de facto standard software.


Want to tweak the pipeline or perform large-scale annotations on your compute cluster? Get Nextflow, the pipeline code under the hood and the Docker dependencies and run the whole workflow on your own machine!


We performed a survey in 2018 contacting 175 users. Overall it was very positive, but assuming we could secure funding, we could improve some aspects of Companion, e.g. more species, more updates, easier upload to EBI, improve accuracy. The results can be seen here.

If you are using Companion in your research, please cite the following publication:

Steinbiss S, Silva-Franco F, Brunk B, Foth B, Hertz-Fowler C, Berriman M, Otto TD
Companion: a web server for annotation and analysis of parasite genomes.
Nucleic Acids Research, 44:W29-W34, 2016.
DOI: 10.1093/nar/gkw292