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Findings from University of California Reveals New Findings on Genomics (Ragout-a reference-assisted assembly tool for bacterial genomes)

August 5, 2014

By a News Reporter-Staff News Editor at Information Technology Newsweekly -- A new study on Genomics is now available. According to news originating from La Jolla, California, by VerticalNews correspondents, research stated, "Bacterial genomes are simpler than mammalian ones, and yet assembling the former from the data currently generated by high-throughput short-read sequencing machines still results in hundreds of contigs. To improve assembly quality, recent studies have utilized longer Pacific Biosciences (PacBio) reads or jumping libraries to connect contigs into larger scaffolds or help assemblers resolve ambiguities in repetitive regions of the genome."

Our news journalists obtained a quote from the research from the University of California, "However, their popularity in contemporary genomic research is still limited by high cost and error rates. In this work, we explore the possibility of improving assemblies by using complete genomes from closely related species/ strains. We present Ragout, a genome rearrangement approach, to address this problem. In contrast with most reference-guided algorithms, where only one reference genome is used, Ragout uses multiple references along with the evolutionary relationship among these references in order to determine the correct order of the contigs. Additionally, Ragout uses the assembly graph and multi-scale synteny blocks to reduce assembly gaps caused by small contigs from the input assembly."

According to the news editors, the research concluded: "In simulations as well as real datasets, we believe that for common bacterial species, where many complete genome sequences from related strains have been available, the current high-throughput short-read sequencing paradigm is sufficient to obtain a single highquality scaffold for each chromosome."

For more information on this research see: Ragout-a reference-assisted assembly tool for bacterial genomes. Bioinformatics, 2014;30(12):302-309. Bioinformatics can be contacted at: Oxford Univ Press, Great Clarendon St, Oxford OX2 6DP, England. (Oxford University Press -; Bioinformatics -

The news correspondents report that additional information may be obtained from M. Kolmogorov, University of California, Dept. of Comp Sci & Engn, La Jolla, CA 92093, United States. Additional authors for this research include B. Raney, B. Paten and S. Pham.

Keywords for this news article include: La Jolla, Genomics, California, United States, Bacterial Genome, North and Central America

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Source: Information Technology Newsweekly

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