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JBrowse & Apollo Overview - for AGR


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This is a brief update about the genome browser JBrowse and the genome annotation editor Apollo, addressed to the members of the Alliance of Genome Resources (AGR).
Learn more about JBrowse at
Learn more about Apollo at

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JBrowse & Apollo Overview - for AGR

  1. 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
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  3. 3. 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
  4. 4. 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.
  5. 5. 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.
  6. 6. 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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  8. 8. 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. Apollo Genome Annotation Editor
  9. 9. Apollo Genome Annotation Editor Functionality overview
  10. 10. Apollo Information Editor
  11. 11. Annotating frameshifts, correcting single-base errors DNA Track ‘User-created Annotations’ Track
  12. 12. Correcting selenocysteine-containing proteins
  13. 13. Apollo: Tracking Edit History
  14. 14. Apollo Genome Annotation Editor
  15. 15. Apollo Genome Annotation Editor
  16. 16. 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
  17. 17. 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
  18. 18. Apollo in the near, near future u Transformation of coordinates. u Visualization and annotation of variants.
  19. 19. Apollo architecture
  20. 20. 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?
  21. 21. Apollo at AGR: opportunities u Capturing feedback from the community u QC of manual annotations u Merging automated and manual annotations, with version control
  22. 22. 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. 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