8:30: Breakfast
9:00: Conference begins. Serafim Batzoglou, Opening Remarks
9:05: Rick Myers, Distinguished Genomics talk
10:00:
Jim Mullikin,
The Phusion Assembly of the Mouse Genome
10:30: Coffee break
10:45: Sante Gnerre, Improving Arachne: how we Assembled the Mouse Genome
11:15: Jade Vinson, Assembly of the highly polymorphic genome of Ciona savigny
11:45: Granger Sutton, Progress on and Experience with Whole Genome Shotgun Assembly
12:15:
Lunch
1:30: Haixu Tang, Using Repeat Graph for Analysis of Alternative Fragment Assemblies and Finishing Experiments
2:00: Degui Zhi, Resolving Difference Between Nearly Identical Repeats in Fragment Assembly
2:30:
Mark Goldberg,
Improving Shotgun Sequencing Through Learning
3:00:
Coffee Break
3:30: Paul Havlak, Assembling Combiner Whole-Genome and BAC Sequences
4:00: Stephen Heber, Splicing graphs and EST assemblies
4:30:
Todd Smith,
Second Generation Software Tools for DNA Sequencing
5:00: End of first day
8:30: Breakfast
9:00: Gene Myers, On the Limits of Assembly
9:30: Olivier Couronne, Comparative Whole Genome Shotgun Assembly
10:00: Mihail Pop, A Hierarchical Approach to Building Contig Scaffolds
10:30:
Coffee break
10:45: Brian Hunt and James Yorke, Improved Overlap Pairing for Shotgun Assembly of Large Genomes
11:15: Steve Goldstein, Improving Assemblers with Graph-based Optimizations and Heuristics
11:45: Eric Arner, Methods for Error Correction in Shotgun Sequencing Assembly
12:15: Lunch
1:30: Open discussion on the benchmarking of genomic shotgun sequencing assemblers. Chair: Jim Kent
3:00:
Coffee Break
3:30: Kim Worley, The End-game: Finishing Whole Genomes
4:00: Aleksandar Milosavljevic, Clone pooling methods for comparative physical mapping and sequencing
4:30: Conference ends