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Church Fif2009

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This is the talk I gave at the 4th annual Sequencing, Finishing, Analysis in the Future meeting. I tried to record my talk onto the slides based on the recording from the meeting, but it didn't work …

This is the talk I gave at the 4th annual Sequencing, Finishing, Analysis in the Future meeting. I tried to record my talk onto the slides based on the recording from the meeting, but it didn't work well. You can view the talk here: http://www.scivee.tv/node/11410 to hook the words up to the slides.

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Transcript

  • 1. Managing and Comparing Assemblies
    DM Church, NCBI
  • 2. Adapted from Drew Sheneman, New Jersey -- The Newark Star Ledger
  • 3. What’s in a name?
    Bob
    Bob
    Bob
    Bob
  • 4. What’s in a name?
    Bob
    123-45-6789
    *
    *http://howmanyofme.com
  • 5. What’s in a name?
    Bob
    Samantha
    Miranda
    Lydia
  • 6. Mouse chrX: 35,000,000-36,000000
  • 7. Mouse chrX: 35,000,000-36,000000
    X
    MGSCv3
    Build 36
  • 8. Unique Identification
    NC_000086.6
  • 9. What’s in a name?
    GRCh37
    hg19
    Zv7
    danRer5
    Build37
    mm8
    NCBIM37
  • 10. What’s in a name?
  • 11. Assemblies with the same name aren’t always the same
    chr21:8,913,216-9,246,964
  • 12. Assemblies with the same name aren’t always the same
    Zv7 chr21:8,913,216-9,246,964 X Mouse Build 36 chrX
  • 13. Genomic Collections to the rescue
    GRCh37
    hg19
    GCA_000001405.1
  • 14. Genome Browser Agreement
    Submitter deposits assembly to GenBank/EMBL/DDBJ
    Assembly QA
    Submitter updates assembly based on QA results
    Browsers pick up assembly from GenBank/EMBL/DDBJ
  • 15. Genome Browser Agreement
    Assemblies must be in
    GenBank/EMBL/DDBJ
  • 16. Decided lack of enthusiasm for new assemblies
    Graves, FF0107
    Oh No! Not a new version of the human genome!
    http://genomereference.org
  • 17. GRCh37
  • 18. Conflict: locus specific users vs. whole genome users
  • 19. How do we decide when to upgrade?
    Phenotypes:
    Developmental Delay
    Head circumference
    Autism
    Schizophrenia
    1q21
    Brunetti-Pierri et al., 2008
  • 20. Any easier way to find the differences
    HG-21
    Description: ESP analysis suggests the reference chromosome contains an inversion within AL139246.20.
    Resolution: AL139246.20 was updated to AL139246.21 on 20 January, 2007. issue reported in this ticket (an inversion)
  • 21. Any easier way to find the differences
  • 22. Any easier way to find the differences
    HG-2
    Build 36, chr 4 (NC_000004.10)
    GAP
    GRCh37, chr4 (CM000666.1)
    GRCh37, alt locus 8 (GL000257.1)
    Xue Y et al, 2008
  • 23. Alignments, Alignments, Alignments
  • 24. Any easier way to find the differences- better alignments
  • 25. Thanks…
    NCBI Genome Pipeline staff
    Avi Kimchi
    Paul Kitts
    Mike DiCuccio
    Nathan Bouk
    Josh Cherry
    Cliff Clausen
    Wratko Hlavina
    Valerie Schneider
    Genome Reference Consortium
    The Genome Center at Washington University
    The Wellcome Trust Sanger Institute
    The European Bioinformatics Institute
    The National Center for Biotechnology Information
  • 26. URLs mentioned in talk
    AGP Specification and Validation
    http://www.ncbi.nlm.nih.gov/genome/assembly/agp/
    Genome Workbench
    http://www.ncbi.nlm.nih.gov/projects/gbench
    Sequence Viewer
    http://www.ncbi.nlm.nih.gov/projects/sviewer
    Genome Reference Consortium
    http://genomereference.org
    How Unique is your name?
    http://howmanyofme.com

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