Abstract
Next Generation Sequencing (NGS) technologies are capable of reading millions of short DNA sequences both quickly and cheaply. While these technologies are already being used for resequencing individuals once a reference genome exists, it has not been shown if it is possible to use them for ab initio genome assembly. In this paper, we give a novel network flow-based algorithm that, by taking advantage of the high coverage provided by NGS, accurately estimates the copy counts of repeats in a genome. We also give a second algorithm that combines the predicted copy-counts with mate-pair data in order to assemble the reads into contigs. We run our algorithms on simulated read data from E. Coli and predict copy-counts with extremely high accuracy, while assembling long contigs.
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Medvedev, P., Brudno, M. (2008). Ab Initio Whole Genome Shotgun Assembly with Mated Short Reads. In: Vingron, M., Wong, L. (eds) Research in Computational Molecular Biology. RECOMB 2008. Lecture Notes in Computer Science(), vol 4955. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-78839-3_5
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DOI: https://doi.org/10.1007/978-3-540-78839-3_5
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-78838-6
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