Apollo: Democratizing genome annotation

Abstract

Genome annotation is the process of identifying the location and function of a genome's encoded features. Improving the biological accuracy of annotation is a complex and iterative process requiring researchers to review and incorporate multiple sources of information such as transcriptome alignments, predictive models based on sequence profiles, and comparisons to features found in related organisms. Because rapidly decreasing costs are enabling an ever-growing number of scientists to incorporate sequencing as a routine laboratory technique, there is widespread demand for tools that can assist in the deliberative analytical review of genomic information. To this end, we present Apollo, an open source software package that enables researchers to efficiently inspect and refine the precise structure and role of genomic features in a graphical browser-based platform. Some of Apollo’s newer user interface features include support for real-time collaboration, allowing distributed users to simultaneously edit the same encoded features while also instantly seeing the updates made by other researchers on the same region in a manner similar to Google Docs. Its technical architecture enables Apollo to be integrated into multiple existing genomic analysis pipelines and heterogeneous laboratory workflow platforms. Finally, we consider the implications that Apollo and related applications may have on how the results of genome research are published and made accessible.

Growing a circular economy with fungal biotechnology: a white paper

“…The future development and continued support of this and other such initiatives should help the lab-based researchers complete a good first draft of a genome annotation efficiently without major resource implications. Furthermore, recent developments in the Apollo pipeline [130], integrated within databases such as VEuPathDB [131], allows researchers to inspect and modify genome features efficiently and can also be utilised in private workspaces. Data can remain private to a specific work group and be transferred to public databases when appropriate.…”

Comparative genomics applied to Mucor species with different lifestyles

“…Non-coding RNA were predicted with tRNAscan-SE [95], RNAmmer [96] and Infernal [97] using the Rfam database [98]. The obtained data were integrated in an instance of the genome viewer Apollo [99] allowing experts to validate gene prediction quality and perform manual curation.…”

Extensive genomic and transcriptomic variation defines the chromosome-scale assembly ofHaemonchus contortus, a model gastrointestinal worm

“…The overall annotation strategy is presented in Additional file 1: Figure S6 and consisted of four key stages: (i) RNAseq evidence was used to train ab initio gene finding using Braker [35] ; (ii) full-length high-quality isoforms generated using Iso-Seq were used to identify candidate gene models using the annotation tool Program to Assemble Spliced Alignments (PASA; [36] ; (iii) evidence from steps (i) and (ii), together with 110 manually curated genes and orthologs from the C. elegans and H. contortus V1 genomes, were incorporated using EvidenceModeller; and finally (iv) UTRs and multi-evidence gene models were updated using the full-length isoforms once again using PASA. We further curated the genome annotation using Apollo [37] ; together, this strategy achieved a high level of sensitivity and precision based on comparison with a subset of manually curated genes ( Additional file 2: Table S5 ).…”

“…The genome annotation, as well as available evidence used to generate the annotation (including per life stage RNAseq, Iso-Seq [full-length high quality & CCS reads], coverage and repeat tracks), was uploaded to the web portal Apollo[37] for further visualisation and manual curation. This platform has been used to provide a means to continually improve the H. contortus genome annotation via manual curation as new information becomes available.…”