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, Apollo is 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.In this paper we first outline some of Apollo's newer user interface features, which were driven by the needs of this expanding genomics community. These 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.

Diaci v3.0: Chromosome-level assembly,de novotranscriptome and manual annotation ofDiaphorina citri,insect vector of Huanglongbing

“…Predicted protein-coding genes were longer compared to OGSv1 gene models with more exons predicted per gene. Curated genes represent manually refined models based on evidence from orthology and expression data using Apollo annotation editor [9]. Curation was performed by distributed groups based on curated workflow previously described in Hosmani et al [14].…”

“…Gene sets involved in chitin metabolism, cuticle formation, segmentation and segmental identity, signal transduction, chromatin remodeling, phototransduction, circadian rhythm, carbohydrate metabolism, melanization and spermatogenesis were manually curated using Apollo annotation editor [9].…”

G-OnRamp: Generating genome browsers to facilitate undergraduate-driven collaborative genome annotation

“…These tools are combined into multi-step workflows that process a target genome assembly and create a UCSC Assembly Hub (which can be viewed at the official UCSC Genome Browser; http://genome.ucsc.edu) or a locally-bundled JBrowse instance. G-OnRamp also provides tools to import a JBrowse instance into Apollo to facilitate real-time collaborative genome annotation (https://genomearchitect.readthedocs.io/en/latest/; [10]). In a pedagogical example, an instructor can deploy G-OnRamp, upload the data, run a workflow to generate a JBrowse genome browser for visualization, and use the G-OnRamp Apollo interaction tools to convert the genome browser hub to Apollo for collaborative analysis by students.…”

“…Gene annotation builds on what students are learning about gene structure, while requiring them to grapple with multiple lines of evidence to establish defendable gene models. Student annotation projects thus are mutually beneficial for researchers and for students, enabling unique science and providing a multi-faceted learning experience for students [6,7,8,9,10].…”

JBrowse Connect: A server API to connect JBrowse instances and users

“…Some of these integrations are re-usable in general contexts. Notably, the Apollo project enables biocurators to collaborate in real time editing genome annotations (Lee et al 2013;Dunn et al 2019) . Bioinformatics web applications such as Tripal (Ficklin et al 2011) and Galaxy (Afgan et al 2016) have extensions that integrate JBrowse to some extent.…”