Utilization of Probabilistic Models in Short Read Assembly from Second-Generation Sequencing

With the advent of cheaper and faster DNA sequencing technologies, assembly methods have greatly changed. Instead of outputting reads that are thousands of base pairs long, new sequencers parallelize the task by producing read lengths between 35 and 400 base pairs. Reconstructing an organism’s genome from these millions of reads is a computationally expensive task. Our algorithm solves this problem by organizing and indexing the reads using n-grams, which are short, fixed-length DNA sequences of length n. These n-grams are used to efficiently locate putative read joins, thereby eliminating the need to perform an exhaustive search over all possible read pairs. Our goal was develop a novel n-gram method for the assembly of genomes from next-generation sequencers. Specifically, a probabilistic, iterative approach was utilized to determine the most likely reads to join through development of a new metric that models the probability of any two arbitrary reads being joined together. Tests were run using simulated short read data based on randomly created genomes ranging in lengths from 10,000 to 100,000 nucleotides with 16 to 20x coverage. We were able to successfully re-assemble entire genomes up to 100,000 nucleotides in length.

Panel Discussion - Local Finns in Illinois

Finnish North American labor contributions and involvement in strikes such as the 1913-14 Michigan Copper Strike are being restored to the historical record and even commemorated; yet some Finnish American communities’ labor history still goes untold. We contend that in the case of DeKalb, Illinois, the Finnish American labor and strike history has been, in part, overshadowed in contemporary remembrance by the city’s promotion of traditional history and commemoration focused on the barbed wire barons. Local Finnish American labor involvement and participation in strikes appears to have been marginalized in favor of a subsequent historical narrative surrounding the capitalist entrepreneurship of elites. However, counter memories of labor struggles may be lost for a variety of reasons. External and internal forces make it difficult for marginalized groups to offer alternatives to the construction of collective memories that exclude them. These forces include, but are not limited to gradual assimilation into dominant culture, internal conflict within social movements, and fear of, or experience with, governmental repression. In our archival research, surveys and interviews with 2nd and 3rd generation Finnish American residents reveal the many forces of “forgetting” that can influence the counter memory of Finnish American labor history in certain communities.