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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1. User-created Annotations2. Evidence Tracks: Experimental data, alignments3. Annotator Panel: Removable dock4. Tabs for searching, editing, and exporting Data5. Switch between organisms and sequences6. Visualize and edit annotation details

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Latest Features

{REST}

Automated AnnotationsGFF3, FASTA, BAM, etc.

GFF3, FASTA, Chado

Next Workflowe.g. Tripal

Manual Annotation1. Import to JBrowse2. Import Organism3. Manual Annotation4. 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

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3 Example of Galaxy / Apollo Integration using Docker

Folded 592 bp

Bringing exons closer together facilitates annotating gene models with long introns.

Web Services ClientPerl, Shell, Groovy, PHP, etc.

{JSON}

GFF3FASTA

Annotators

JBrowse Directories

WebSockets{REST}and

{REST}

File System JDBC

Apollo componentsCustomizable

Security

Apollo Server - Grails

Controllers

Views (gsp) Services & Plug-in Domains

SiteMesh(OpenSymphony)

GORM

Hibernate

HSQLDB

Java Enterprise Edition Groovy

Java Virtual Machine

Gan

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Scaffold 2Scaffold 1

Genome Assembly

. . . . . . Scaffold n

212,500 214,000

GB40027-RA GB40022-RA

GB40028-RA

Scaffold 223 Scaffold 171,350,000

Scaffold details

Scaf

fold

det

ails

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