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Assemblathon 2 wins open data award
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Tuesday, April 22, 2014
By Branwyn Wagman, UC Santa Cruz
The Assemblathon 2 paper in the journal Gigascience won the Open Data Award from the 2013 BioMed Central Annual Research Awards. The award, sponsored by LabArchives, recognizes leadership in tackling the challenges associated with open sharing of research results.
Co-corresponding author Keith Bradnam from the Genome Center at University of California, Davis, expressed delight that the project's efforts at transparency were recognized. "When scientists make it easier for others to download their datasets, access the code used to generate data, and read a draft of a manuscript prior to publication, then everyone wins. All science should be open science."
Assemblathons are contests to assess state-of-the-art methods in the field of genome assembly. The Assemblathon 2 attempted to sift through the myriad tools currently available for combining raw genome sequencing data into high-quality, finished genome sequences. The competition used real data from three vertebrate species—a bird, a fish, and a snake.
In the Assemblathon 2 competition, 21 teams from throughout the world submitted a total of 43 assemblies, and teams from UC Davis, UC Santa Cruz, and Wellcome Trust Sanger Institute assessed the assemblies based on ten different criteria.
At the end of the Assemblathon 2 competition, the participants met at the biennial Genome 10K project meeting and produced the paper that won the award.
The competition did not result in a clear winner, so the paper outlined the pros and cons of the more effective methods.
Bradnam said, "To paraphrase Abraham Lincoln: you can get an assembler to perform well across all metrics in some species or across some metrics in all species, but you can’t get an assembler to perform well across all metrics in all species.”
The Assemblathon is a collaborative, recurring effort to spur improvements in computational methods for genome assembly. Teams use their own software to assemble one or more genomes that the organizers of the Assemblathon make available. All participants have the same amount of time to try to assemble the genomes, and then the organizers evaluate each group's efforts.
The Genome 10K project launched the first Assemblathon in 2010. Assemblathon 2 started in 2011, and the manuscript was published in July 2013.