At his Not Invented Here blog, Harvard School of Public Health's Oliver Hofmann discusses the Broad Institute's David Jaffe's keynote talk at Beyond the Genome 2011's Genome Informatics Pre-Meeting held in Washington, DC, this week. Hofmann summarizes Jaffe's key points on genome assembly challenges during this time of "rapid technological change." According to Hofmann, Jaffe stressed that toward the end-goal of improved linear assemblies, changes to format requirements are needed. For example, assemblies should encompass an "inner layer which includes annotation [and] local graphs" as well as an "outer layer that contains information on the global structure — e.g., information about perfect repeats that cannot be resolved." Hofmann says Jaffe noted that gap size estimation continues to be a challenge, one that may necessitate "local re-assemblies around problem spots or inconsistencies" going forward. Overall, Hofmann summarizes Jaffe's talk, saying that the "potential of current data not 'maxed out' yet." The data, Hofmann writes, "can be traced and improved by better algorithms," though he adds that "part of the solution has to come through a better representation of genomes."
Sep 21, 2011