Argonne National Laboratory

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Algorithms and Services for Genome Assembly

Computational Institute Presentation
Fangfang Xia (MCS)
July 25, 2013 1:00PM to 2:00PM
University of Chicago, Searle Lab 240A
This talk will be broadcast to Argonne in Building 240 TCS, Room 5172.

Genome assembly is the process of reconstructing entire DNA sequences from fragmentary input. While high-throughput sequencing technology has revolutionized the field of genomic science, assembly, often the first step of many bioinformatics pipelines, remains a computationally expensive problem which is further compounded by the difficulty to evaluate its accuracy. In this talk, I will describe the assembly algorithms, applications and practices. I will focus on a parallel tool we have developed for metagenomic assembly and discuss how it could be improved by building on a kmer-matching library. Finally, I will touch on an extensible pipeline service we are developing to help users find the best assembly.

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