jbrowse & apollo overview - for agr

JBrowse & ApolloMonica Munoz-Torres, PhD | @monimunozto

for the JBrowse & Apollo Development Teams

Berkeley Bioinformatics Open-source Projects Environmental Genomics and Systems Biology Division

Lawrence Berkeley National LaboratoryAGR Curation Call | 7 December 2016

UNIVERSITY OF CALIFORNIA

http://jbrowse.org/

JBrowse

u Fast, embeddable genome browseru Smooth scrolling and zooming

u Built to handle large genomes and deep-coverage sequencingu Supports:

GFF3, BED, FASTA, Wiggle, BigWig, BAM, VCF (with tabix), REST, etc. u Faceted tracks optionu Light server requirements

http://jbrowse.org/

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.

JBrowse in the near future

u Analytics u e.g. J-BLAST, Galaxy integration* (Docker)

u JB will grow a server-sideu Pub-sub messagingu Dashboards:

u phylogeography,

u systems biology,

u molecular evolution.

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.

http://GenomeArchitect.org/

ColorbyCDSframe,togglestrands,setcolorschemeandhighlights.

Uploadevidencefiles(GFF3,BAM,BigWig),addcombination andsequencesearchtracks.

QuerythegenomeusingBLAT.

Navigationandzoom.Searchforagenemodelorascaffold.

User-createdannotations.Annotatorpanel.

EvidenceTracks.

Stageandcell-typespecifictranscriptiondata.

Admin

Protein coding, pseudogenes, ncRNAs, regulatory elements, variants, etc.

Collaborative, instantaneous, web-based, built on top of JBrowse.

GenomeArchitect.org

Apollo Genome Annotation Editor


Functionality overview

Apollo Information Editor

Annotating frameshifts, correcting single-base errors

DNATrack

‘User-createdAnnotations’Track

Correcting selenocysteine-containing proteins

Apollo: Tracking Edit History


GenomeArchitect.org

1. Bringing exons closer together to facilitate annotation of gene models with long introns.

1,275bp

Concept for Apollo v2.1 – Northern Spring 2017

Apollo in the near future:Transformation of coordinates

2. Assembly artifacts may cause gene models to be split across two or more scaffolds. Apollowill 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

Apollo in the near, near future

u Transformation of coordinates. u Visualization and annotation of variants.

Apollo architecture

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?

Apollo at AGR: opportunities

u Capturing feedback from the communityu QC of manual annotationsu Merging automated and manual annotations, with version

control

Berkeley Bioinformatics Open-Source Projects, Environmental Genomics & Systems Biology, Lawrence Berkeley National Laboratory

Suzanna Lewis Chris Mungall Seth CarbonNathan Dunn

Monica Munoz-Torres

Jeremy Nguyen Xuan

Fundingu 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


berkeleybop.org
