@apollo_bbop Demo:

D02

Apollo: Collaborative and Scalable

Manual Genome Annotation
1 1 2
Nathan A. Dunn , Monica C. Munoz-Torres , Deepak Unni ,
4 5 3 3
Eric Rasche , Anthony Bretaudeau , Eric Yao , Ian Holmes ,
2 1
Christine G. Elsik and Suzanna E. Lewis
(1) Lawrence Berkeley National Laboratory, Berkeley, CA, (2) Division of Animal Sciences, University of
Missouri, Columbia, MO, (3) Department of Bioengineering, Berkeley, CA, , (4) Center for Phage Technology,
Department of Biochemistry and Biophysics, Texas A & M University, College Station, TX, (5) BIPPA, Rennes, FR

http://genomearchitect.org /

h t t p s : / /g i t h u b . o r g / G M O D /A p o l l o /
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Example Genome Analysis Workflow

Sequencing Create Automated
Assembly Annotation

FGENESH

Experimental design, Manual

sampling Annotation

Comparative analyses

Synthesis &
dissemination
Curated
Gene Set

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Example Genome Analysis Workflow

Sequencing Create Automated
Assembly Annotation

FGENESH

Experimental design, Manual

sampling Annotation

Comparative analyses

Synthesis &
dissemination
Curated
Gene Set

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Annotation
Structural Annotation Functional Annotation
• exons, introns, UTRs • metabolic pathways / functions
• repeat regions • Gene Ontology
• transposable elements • molecular function
• tRNA, snRNA, snoRNA, miRNA, • biological process
ncRNA, rRNA • cellular component
• expression
• gene families

http://geneontology.org

Photo Credit: Alex Wild at http://www.alexanderwild.com/

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Analysis Requires High Quality Data

Sequencing Create Automated
Assembly Annotation

d FGENESH

Experimental design, Manual

sampling Annotation

Comparative analyses

Synthesis & Consensus

dissemination Gene Set

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Automated Identification is not Perfect

Generation of Gene Models
Automated Find ORFs, multiple rounds of gene prediction
Annotation
Annotation of Gene Models

Predicting function, expression patterns,
metabolic network memberships

Manual
Annotation

• Assembly errors can cause fragmented annotations

• Limited coverage makes precise identification difficult 6
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Manual Annotation Refines Genome

Automated
Annotation

cDNAs, HMM domain searches, RNAseq,

genes from other species.
Experimental Evidence

Manual
Annotation

Human Analysis

• Additional data
• Biological knowledge
• Curator best represents underlying evidence 7
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Analysis Requires High Quality Data

Sequencing Create Automated
Assembly Annotation

d FGENESH

Experimental design, Manual

sampling Annotation

Comparative analyses

Synthesis & Consensus

dissemination Gene Set

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Analysis Requires High Quality Data

Sequencing Create Automated
Assembly Annotation

d FGENESH

Experimental design, Manual

sampling
•Understand Error Annotation

•Reduce Error
Comparative analyses

Synthesis & Consensus

dissemination Gene Set

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Apollo is Used to Produce High Quality Annotations

• Over 100 organizations use Apollo
• Multiple genomes and labs per server

Refined Annotations Distributed to Public

NCBI Ensembl
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Apollo is a Tool for Collaborative Annotation

Annotators • Web-based Editor
Apollo
Google Web Toolkit
(GWT) / Bootstrap
• Visual feedback
• Real-time collaborative
• genomic browser

Annotators

Annotators Apollo
Google Web Toolkit
Apollo (GWT) / Bootstrap
Google Web Toolkit
(GWT) / Bootstrap

Photo Credits: i5K; Alex Wild at http://www.alexanderwild.com/: leaf cutter ant, ensign wasp; Leo Bukeboom:
Nasonia vitripennis jewel wasp; Wikimedia Commons: Apis mellifera honey bee; Mike MacNeil USDA/ARS Fort
Keogh LARRL: Bos taurus cow. 11
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1 - Evidence Viewer (Genome Browser)

Manual Annotation

Transcripts
(GFF3, GBK)

BAM Reads

Automated
Evidence
Annotation

Transcripts
Themes (GFF3, GBK)
(dark/light)
BigWig XY

Color CDS Frame BigWig

HeatMap
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1 - Evidence Viewer (Genome Browser)

Configure Multiple Tracks
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1 - Evidence Viewer (Genome Browser)

Dynamically Open
Configure Multiple Tracks

Append via URL

addStores={"url":{"type":"JBrowse/Store/SeqFeature/
GFF3","urlTemplate":"http://host/genes.gff"}}
&addTracks=[{"label":"genes","type":"JBrowse/View/
Track/CanvasFeatures","store":"url"}]

Statically Configure
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1 - Evidence Viewer (Genome Browser)

Dynamically Open
Configure Multiple Tracks
• BAM
• BigWig
• GFF
• GTF
• GBK
• VCF
Append via URL • FASTA
• FASTAi
addStores={"url":{"type":"JBrowse/Store/SeqFeature/
GFF3","urlTemplate":"http://host/genes.gff"}}
&addTracks=[{"label":"genes","type":"JBrowse/View/
• SPARQL
Track/CanvasFeatures","store":"url"}]
• custom types
(e.g., REST end-
point)
Statically Configure

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1 - Evidence Viewer (Genome Browser)

Dynamically Open
Configure Multiple Tracks
• BAM
• BigWig
• GFF
• GTF
• GBK
• VCF
Append via URL • FASTA
• FASTAi
addStores={"url":{"type":"JBrowse/Store/SeqFeature/
GFF3","urlTemplate":"http://host/genes.gff"}}
&addTracks=[{"label":"genes","type":"JBrowse/View/
• SPARQL
Track/CanvasFeatures","store":"url"}]
• custom types
(e.g., REST end-
point)
Statically Configure

Customizable Views https://gmod.github.io/jbrowse-registry/

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https://gmod.github.io/jbrowse-registry/

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https://gmod.github.io/jbrowse-registry/

• Demo Link
• GitHub Repo
• Configure Apollo
to install easily

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Select an existing feature

JBlast
Workflow monitor

Highlight Arbitrary Region

• Support any analysis server

• Support local execution

• JBlast “Example” Galaxy BLAST Implementation

• Apollo supports BLAT / BLAST, but this will be better
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2 - Genome Annotation Editor

Manual Annotation
Exported Refined
Transcripts
Genomic Elements
(GFF3, GBK)

BAM Reads

Automated
Annotation

Transcripts
(GFF3, GBK)
BigWig XY

BigWig
HeatMap
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Create Annotation
Add Annotation by Annotate other genomic
Dragging a Genomic Element types with drop-down

Alignments shown in red

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Edit Annotation Structure

Adjust exon by dragging

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Editing Annotations
Change Annotation Edit Associations
Type
• PubMed / dbxref
• Gene Ontology
• Metadata
• key/value
• status
Edit Additional
Structural Data • comments
(right-click popup)

History of
Structural Edits 23
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Edit Annotation Structure

Revertible History of Structural Operations

Highlighted row shown

Current position

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Annotate Reference Sequence Alterations

Alteration Reflected

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3 - Annotator Panel
Link to
Location
Collapsible
Navigate Sequence and Organism

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Annotation Tab - Alternate View

Search

List / Navigate Vertically

View / Edit Details 27

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Reference Sequence - Search and Export

Search

Export Annotations

Navigation

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Organism: Configuration
Create JBrowse tracks from FASTA / GFF3 / BAM / BigWig
Genome Res. 2009 Sep;19(9):1630-8. doi: 10.1101/gr.094607.109

Import JBrowse directory

Share “Public” organisms
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Users and Groups

Add / Search Users

Use Groups to
Edit User Manage Bulk
Permission Permissions

User Can “Admin” an Organism 30

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Admin Panel

Predefine Curation Terms

Reports

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Summary of Features
Genome Annotation Editor
History Structural + Functional
Visual Feedback Annotator Panel

Evidence Viewer Alternate view of data

Simplified administration

Customizable

Multiple data types

Easy to navigate

Fast
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Architecture
Annotators

Apollo
Web Services Client JBrowse Apollo Google Web Toolkit
(GWT) / Bootstrap
DOJO / jQuery

Perl, Shell, Groovy, PHP, etc.

Client(s) WebSocket

REST

Security Server
Apollo Server - Grails

File
System

JDBC

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Architecture
Annotators

Apollo
Web Services Client JBrowse Apollo Google Web Toolkit
(GWT) / Bootstrap
DOJO / jQuery

Perl, Shell, Groovy, PHP, etc.

Client(s) WebSocket

REST

Security Server
Apollo Server - Grails

File
System

JDBC

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Architecture
Annotators

Apollo
Web Services Client JBrowse Apollo Google Web Toolkit
(GWT) / Bootstrap
DOJO / jQuery

Perl, Shell, Groovy, PHP, etc.

Client(s) WebSocket

REST

Security Server
Apollo Server - Grails

File
System

JDBC

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Architecture
Annotators

Apollo
Web Services Client JBrowse Apollo Google Web Toolkit
(GWT) / Bootstrap
DOJO / jQuery

Perl, Shell, Groovy, PHP, etc.

Client(s) WebSocket

REST

Security Server
Apollo Server - Grails

File
System

JDBC

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Integration Strategies
• Configure apollo-config.groovy
• Grails plugin
• JBrowse plugin
• Database
• Fork h t t p s : / /g i t h u b . o r g / G M O D /A p o l l o /

• Ask apollo@lists.lbl.gov

• Web services

Perl, Shell, Groovy, PHP, etc. 37

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Scriptable Web Services

• Examples: Groovy, Perl, shell, Python
• Autogenerated REST API doc in Apollo

curl -d "{ 'operation': 'get_features',

‘track':'Group1.10','username':'ndunn@me.c
om','password':'demo'}" http://localhost:
8080/apollo/AnnotationEditorService

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Workflow
Automated Annotations
GFF3 FASTA BAM, etc

JBrowse

Manual Annotation

GFF3 FASTA CHADO

TRIPAL
Next Workflow
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Automated Annotations
GFF3 FASTA BAM, etc

Manual Annotation

GFF3 FASTA CHADO

TRIPAL?
Next Workflow 40
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View directly in <server>:<port>/apollo/

https://github.com/GMOD/docker-compose-galaxy-annotation

2
1

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View directly in <server>:<port>/apollo/

https://github.com/GMOD/docker-compose-galaxy-annotation
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2
1

3
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Other Integration Projects

https://github.com/galaxy-genome-annotation/
• Pre-built workflow with Annotation Tools, Dockerized
• Genome Annotation Birds of a Feather Session at 6 pm.

https://github.com/galaxy-genome-annotation/python-apollo
• Arrow from Parsec, python library that wraps web-services
$ arrow groups create_group university
{
"publicGroup": false,
"class": "org.bbop.apollo.UserGroup",
"name": "university",
"users": null,
"id": 558319
}
$ arrow users get_users | \
jq '.[] | select(.username | contains("@tamu.edu")) | .username' | \
xargs -n1 arrow users add_to_group university

https://github.com/GMOD/docker-apollo
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Summary
Curators refine genome annotations Apollo
Google Web Toolkit
(GWT) / Bootstrap Real-time collaborative

Annot
Apollo
Google Web Toolkit
Apollo (GWT) / Bootstrap
Google Web Toolkit
(GWT) / Bootstrap

Integrates within workflow

Visual evidence and feedback

FGE
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Future Work: Projection

Genome Folding

Phenotype
2.3 annotation

Variant annotation
2.2 and visualization

2.1 Projection
Assembly Composition
DB backend, Sidebar,
2.0 Grails, Multi- Group 20 Group 31

organism, WS

1.0 Mavenize

Web Apollo
Desktop Apollo

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Reverse Complement: 2.1.0 (Jul/Aug)

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Reverse Complement: 2.1.0 (Jul/Aug)

Reverse Full Annotations

Available In JBrowse Mode

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Genome Folding (2.1.1)

Fold Between Exons Fold All Introns

View Sequence Boundaries

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Genome Folding (2.1.1)

Fold Between Exons Fold All Introns

View Sequence Boundaries

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Fold Individual Features (2.1.2)

View Individual Features

Indicates Folds
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Assembly Composition (2.1.3)

Select to Drag to Rearrange
Combine

Flip Entire
Used Scaffolds
Orientation

Set Orientation

Partial Scaffold
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Cross-Scaffolds Operations

Modify Exon Boundary

Merge
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Variant Annotation and Visualization (2.2)

Annotate Variants

Phenotype
2.3 annotation

Variant annotation
2.2 and visualization

2.1 Projection
Create from Evidence (e.g., VCF)
DB backend, Sidebar,
2.0 Grails, Multi- Visual Predictions
organism, WS

1.0 Mavenize

Web Apollo
Desktop Apollo
 @apollo_bbop Demo: D02
Manual Refinement
• Berkeley Bioinformatics Open-source Projects (BBOP),
Berkeley Lab: Apollo and Gene Ontology teams. Suzanna E.
Lewis (PI).
• § Christine G. Elsik (PI). University of Missouri.
Better Data • * Ian Holmes (PI). University of California Berkeley.
Apollo/BBOP Galaxy • Apollo is supported by NIH grants 5R01GM080203 from
NIGMS, and 5R01HG004483 from NHGRI. Also supported
*Nathan Dunn Eric Rasche by the Director, Office of Science, Office of Basic Energy
Monica Munoz- Sciences, of the U.S. Department of Energy under Contract
Anthony
Torres No. DE-AC02-05CH11231
Bretaudeau
Deepak Unni § • Alex Wild at http://www.alexanderwild.com/: leaf cutter
Björn Grüning ant, ensign wasp; Leo Bukeboom: Nasonia vitripennis jewel
Suzi Lewis wasp; Wikimedia Commons: Apis mellifera honey bee;
GO (BBOP)
JBrowse Mike MacNeil USDA/ARS
Chris Mungall
Eric Yao • Thanks to you and the Apollo / GMOD
Seth Carbon
Ian Holmes Communities
Jeremy Nguyen

• http://genomearchitect.org
• https://github.org/GMOD/Apollo/
 @apollo_bbop Demo: D02
Manual Refinement
• Berkeley Bioinformatics Open-source Projects (BBOP),
Berkeley Lab: Apollo and Gene Ontology teams. Suzanna E.
Lewis (PI).
• § Christine G. Elsik (PI). University of Missouri.
Better Data • * Ian Holmes (PI). University of California Berkeley.
Apollo/BBOP Galaxy • Apollo is supported by NIH grants 5R01GM080203 from
NIGMS, and 5R01HG004483 from NHGRI. Also supported
*Nathan Dunn Eric Rasche by the Director, Office of Science, Office of Basic Energy
Monica Munoz- Sciences, of the U.S. Department of Energy under Contract
Anthony
Torres No. DE-AC02-05CH11231
Bretaudeau
Deepak Unni § • Alex Wild at http://www.alexanderwild.com/: leaf cutter
Björn Grüning ant, ensign wasp; Leo Bukeboom: Nasonia vitripennis jewel
Suzi Lewis wasp; Wikimedia Commons: Apis mellifera honey bee;
GO (BBOP)
JBrowse Mike MacNeil USDA/ARS
Chris Mungall
Eric Yao • Thanks to you and the Apollo / GMOD
Seth Carbon
Ian Holmes Communities
Jeremy Nguyen

• http://genomearchitect.org
• https://github.org/GMOD/Apollo/
Extra Slides