W564
Assembly Improvements to Move Beyond Loblolly Pine Assembly v1.0

Date: Saturday, January 11, 2014
Time: 11:30 AM
Room: Pacific Salon 6-7 (2nd Floor)
Aleksey Zimin , Institute for Physical Science and Technology, University of Maryland, College Park, MD
Steven L Salzberg , Johns Hopkins University, School of Medicine, Baltimore, MD
Daniela Puiu , Johns Hopkins University, School of Medicine, Baltimore, MD
Kristian Stevens , Department of Evolution and Ecology, University of California, Davis, Davis, CA
Michael Roberts , Univeristy of Maryland, College Park, MD
James A Yorke , University of Maryland, College Park, MD
Guillaume Marcais , Insitutte for Physical Science and Technology, College Park, MD
Chuck Langley , University of California, Davis, Davis, CA
PDF file
In the early 2013 we produced an assembly of 22Gb Loblolly pine genome version 1.01.  Currently this is the most contiguous large conifer genome assembly with N50 contig size of over 8kb.  We used MaSuRCA genome assembler developed at the University of Maryland to assemble nearly 15B Illumina reads. After analyzing intermediate assembly results we learned that this assembly can be significantly improved by generating additional data and applying improved assembly techniques.  In this presentation we discuss the results of our analysis that show that the paired end reads with larger library fragment sizes can potentially make the greatest impact for improving the assembly.  We also show how we improved the data filtering and assembly steps based on the analysis of the assembly results. We present the impact of the improved assembly techniques on the test data sets. Our goal is to produce a much improved loblolly pine reference genome by the mid-2014.
Back to: Pine Genome Reference Sequence
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