Easy and reliable parasite genome annotation.

Annotate your sequence!

or find your job by ID:

New Companion Instance.

A new Companions instance is available as the University of Glasgow. It has more resources and we hope to update the reference base. Further, it is generate reduncancy.


Annotation of a new genome could be as easy as uploading your scaffold sequences (FASTA, EMBL, GenBank), choosing a reference (from our set of 61 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!

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 et al.
Companion: a web server for annotation and analysis of parasite genomes.
Nucleic Acids Research, 44:W29-W34, 2016.
DOI: 10.1093/nar/gkw292

For updates, follow us on twitter: CompanionServer.