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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 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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Church Fif2009

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

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