JBrowse & Apollo Overview - for AGR
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Transcript of JBrowse & Apollo Overview - for AGR
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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
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http://jbrowse.org/
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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/
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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.
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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.
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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.
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http://GenomeArchitect.org/
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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
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Apollo Genome Annotation Editor
Functionality overview
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Apollo Information Editor
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Annotating frameshifts, correcting single-base errors
DNATrack
‘User-createdAnnotations’Track
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Correcting selenocysteine-containing proteins
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Apollo: Tracking Edit History
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Apollo Genome Annotation Editor
GenomeArchitect.org
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GenomeArchitect.org
Apollo Genome Annotation Editor
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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
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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
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Apollo in the near, near future
u Transformation of coordinates. u Visualization and annotation of variants.
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Apollo architecture
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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?
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Apollo at AGR: opportunities
u Capturing feedback from the communityu QC of manual annotationsu Merging automated and manual annotations, with version
control
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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
UNIVERSITY OF CALIFORNIA
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berkeleybop.org
UNIVERSITY OF CALIFORNIA