Apollo Genome Annotation Editor: Latest Updates, Including New Galaxy Integration

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. 1 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 5 5 5 4 6 Latest Features {REST} Automated Annotations GFF3, FASTA, BAM, etc. GFF3, FASTA, Chado Next Workflow e.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 2 Scaffold 1 Genome Assembly . . . . . . Scaffold n 212,500 214,000 GB40027-RA GB40022-RA GB40028-RA Scaffold 223 Scaffold 17 1,350,000 Scaffold details Scaffold details 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 Torres 1 , Nathan A Dunn 1 , Deepak Unni 2 , Eric Yao 3 , Eric Rasche 4 , Colin Diesh 2 , Christine E Elsik 2 , Ian Holmes 3 , Suzanna E Lewis 1 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

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Transcript of Apollo Genome Annotation Editor: Latest Updates, Including New Galaxy Integration

Page 1: Apollo Genome Annotation Editor: Latest Updates, Including New Galaxy Integration

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.

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

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

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

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