The document outlines the features and future developments of the JBrowse and Apollo genome annotation tools, detailing their capabilities in handling large genomes and supporting various data formats. It emphasizes JBrowse's transition to a more versatile JavaScript client and the enhancements planned for Apollo, including better coordination transformations and generalized annotation features. Both tools are supported by several NIH grants and are utilized by numerous institutions globally.

1. JBrowse & Apollo
Monica Munoz-Torres, PhD | @monimunozto
for the JBrowse & Apollo Development Teams
Berkeley Bioinformatics Open-source Projects
Environmental Genomics and Systems Biology Division
Lawrence Berkeley National Laboratory
AGR Curation Call | 7 December 2016
UNIVERSITY OF
CALIFORNIA

2. http://jbrowse.org/

5. JBrowse
u Fast, embeddable genome browser
u Smooth scrolling and zooming
u Built to handle large genomes and deep-coverage sequencing
u Supports:
GFF3, BED, FASTA, Wiggle, BigWig, BAM, VCF (with tabix), REST, etc.
u Faceted tracks option
u Light server requirements
http://jbrowse.org/

6. Currently in JBrowse:
u Continuing to phase out BioPerl - used for consuming Chado, flat
files, JBrowse-specific JSON-based index files, etc.
u Changing to JavaScript client, more versatile, easier to feed data
from a server.
u Supports Canvas tracks for added flexibility to display data; also
working on SVG-based tracks.
u Currently a static site generator, which favors performance.

7. JBrowse in the near future
u Analytics
u e.g. J-BLAST, Galaxy integration* (Docker)
u JB will grow a server-side
u Pub-sub messaging
u Dashboards:
u phylogeography,
u systems biology,
u molecular evolution.

8. JBrowse and AGR: opportunities
u JBrowse instance for AGR to facilitate browsing data
from all organisms; also to standardize export, as *most*
data types from all available organisms can be
downloaded from JB.
u AGR 1.3 - generating AGR JBrowse / Genome features.
u projected for end (Sept) of 2017.

9. http://GenomeArchitect.org/

10. Color by CDS frame, toggle strands,
set color scheme and highlights.
Upload evidence files (GFF3, BAM, BigWig),
add combination and sequence search tracks.
Query the genome using BLAT.
Navigation and zoom.
Search for a gene model
or a scaffold.
User-created annotations.
Annotator panel.
Evidence Tracks.
Stage and cell-type
specific transcription
data.
Admin
Protein coding, pseudogenes, ncRNAs,
regulatory elements, variants, etc.
Collaborative, instantaneous, web-
based, built on top of JBrowse.
GenomeArchitect.org
Apollo Genome Annotation Editor

11. Apollo Genome
Annotation Editor
Functionality overview

12. Apollo Information Editor

13. Annotating frameshifts, correcting single-base errors
DNA Track
‘User-created Annotations’ Track

14. Correcting selenocysteine-containing proteins

15. Apollo: Tracking Edit History

16. Apollo Genome Annotation Editor
GenomeArchitect.org

17. GenomeArchitect.org
Apollo Genome Annotation Editor

18. 1. Bringing exons closer together to facilitate
annotation of gene models with long introns.
1,275 bp
Concept for Apollo v2.1 – Northern Spring 2017
Apollo in the near future:
Transformation of coordinates

19. 2. Assembly artifacts may cause gene models to be split across two or more scaffolds. Apollo
will allow generation of an artificial space where the annotation can be completed.
Scaffold 2Scaffold 1
Genome
Assembly
. . . . . .
Scaffold n
Apollo in the near future:
Transformation of coordinates

20. Apollo in the near, near future
u Transformation of coordinates.
u Visualization and annotation of variants.

21. Apollo architecture

22. u Currently being used at:
i5k, VectorBase, Hymenoptera Genome Database, LepBase,
WormBase (testing), etc.
u ~ 3,000 sessions worldwide in the past month (Nov-Dec 2016)
u 830 users
u ~2,000 sessions in the US
u 200 in UK (Wellcome Trust Sanger Institute is one of biggest JBrowse users)
u 150 in South Korea
u Etc.
Who is using Apollo?

23. Apollo at AGR: opportunities
u Capturing feedback from the community
u QC of manual annotations
u Merging automated and manual annotations, with version
control

24. Berkeley Bioinformatics Open-Source Projects,
Environmental Genomics & Systems Biology,
Lawrence Berkeley National Laboratory
Suzanna Lewis Chris Mungall
Seth Carbon
Nathan Dunn
Monica Munoz-Torres
Jeremy Nguyen Xuan
Funding
u Work for GOC is supported by NIH grant 5U41HG002273-
14 from NHGRI.
u Apollo is supported by NIH grants 5R01GM080203 from
NIGMS, and 5R01HG004483 from NHGRI.
u BBOP is also supported by the Director, Office of
Science, Office of Basic Energy Sciences, of the U.S.
Department of Energy under Contract No. DE-AC02-
05CH11231
For your attention, Thank You.
berkeleybop.org
Collaborators:
- Ian Holmes, Eric Yao - UC Berkeley
- Gene Ontology Consortium
- Monica Poelchau - USDA/NAL
- Chris Elsik, Deepak Unni - University of Missouri
- i5k Steering Group & Community
UNIVERSITY OF
CALIFORNIA

25. berkeleybop.org
UNIVERSITY OF
CALIFORNIA