This document describes Apollo, an open-source web-based tool for collaborative genome annotation. It allows users to curate gene models for multiple organisms on one server, generates analysis-ready data and reports. Key features include user annotations, evidence tracks, an annotator panel, search/edit/export functions, switching between organisms, and visualizing/editing annotation details. Apollo integrates with JBrowse and can export annotations to GFF3, FASTA, and Chado databases.

1. Collaborative, instantaneous, web-
based, built on top of JBrowse.
Apollo supports curation of gene models for
multiple organisms in one server and generates
analysis-ready data as well as progress reports.
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2
3
1. User-created Annotations
2. Evidence Tracks: Experimental data, alignments
3. Annotator Panel: Removable dock
4. Tabs for searching, editing, and exporting Data
5. Switch between organisms and sequences
6. Visualize and edit annotation details
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5
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Latest Features
{REST}
Automated Annotations
GFF3, FASTA, BAM, etc.
GFF3, FASTA, Chado
Next Workflowe.g. Tripal
Manual Annotation
1. Import to JBrowse
2. Import Organism
3. Manual Annotation
4. Export Annotations
Export and update
a Chado database
Annotate multiple
organisms per server
Change type of genomic
element to annotate
gene
pseudogene
ncRNA
Galaxy / Apollo
Integration
1
2
4
3 Example of Galaxy / Apollo Integration using Docker
Folded 592 bp
Bringing exons closer together
facilitates annotating gene models
with long introns.
Web Services Client
Perl, Shell, Groovy, PHP, etc.
{JSON}
GFF3
FASTA
Annotators
JBrowse Directories
WebSockets
{REST}and
{REST}
File
System JDBC
Apollo components
Customizable
Security
Apollo Server - Grails
Controllers
Views (gsp) Services & Plug-in Domains
SiteMesh
(OpenSymphony)
GORM
Hibernate
HSQLDB
Java Enterprise Edition Groovy
Java Virtual Machine
Gant
Scaffold 2Scaffold 1
Genome
Assembly
. . . . . .
Scaffold n
212,500 214,000
GB40027-RA GB40022-RA
GB40028-RA
Scaffold 223 Scaffold 17
1,350,000
Scaffolddetails
Scaffolddetails
Annotation
across scaffolds
Artificially joining scaffolds
facilitates annotation of gene models
split across two or more scaffolds.
Transforming Coordinates
UNIVERSITY
of MISSOURI
Mónica C Muñoz Torres1, Nathan A Dunn1, Deepak Unni2, Eric Yao3,
Eric Rasche4, Colin Diesh2, Christine E Elsik2, Ian Holmes3, Suzanna E Lewis1
1 Lawrence Berkeley National Laboratory, Genomics Division, Berkeley, CA. 2 University of Missouri, Divisions of Plant and Animal Sciences, Columbia, MO.
3 University of California Berkeley, Bioengineering, Berkeley, CA. 4 Center for Phage Technology, Texas A & M University, College Station, TX.
GenomeArchitect.org github.com/GMOD/Apollo @apollo_bbop