Tools for Community Genome Annotation: ZMap and Otter

The HAVANA team produces manual annotation of protein coding genes, long non-coding RNAs, pseudogenes and other specialised biotypes for genomic sequence. We also provide the research community with software, training and our annotation tools that can be used remotely by external collaborators.

Our annotation software, ZMap/Otter, communicates with our server over HTTP, and enables annotators to work anywhere. The server controls data access and allows multi-user annotation, whilst the client holds a local copy of the section of genome that is being annotated. Genomic sequence is run though our custom analysis pipeline and this is displayed in our graphical visualisation tool ZMap, which communicates with Otter to create and store the annotation. ZMap can also connect directly to Ensembl and users can create annotation as GFF3. ZMap/Otter is available as a Mac or Linux client, or for Windows users we have a virtual machine image that is installed and run using VirtualBox (https://www.virtualbox.org/). The resulting annotation is either subject to internal quality control (Gatekeeper model) or downloaded directly (Blessed annotator model) (Loveland et al 2012).

The approved gene sets are hosted on the publicly available VEGA browser (http://vega.sanger.ac.uk/) and can be merged into the Ensembl gene set. We follow the Ensembl quarterly release cycle, however, the implementation of an update track hub (ftp://ngs.sanger.ac.uk/production/gencode/update_trackhub/hub.txt)

enables browsers to show recently annotated genes (updated every 24 hours) without waiting for the next full release of the gene set.

Our annotation software is freely available via our website (http://www.sanger.ac.uk/resources/software/otterlace/).