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.

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