apollo genome annotation editor: latest updates, including new galaxy integration
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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
t
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
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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