Hamed Salooti

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The rapidly diminishing cost of genome sequencing is driving renewed interest in large scale genome sequencing programs such as <i>Genome 10K</i> (G10K). Despite renewed interest the assembly of large genomes from short reads is still an extremely resource intensive process. This work presents a scalable algorithms to create scaffolds, or ordered and(More)
Interest in de novo genome assembly has been renewed in the past decade due to rapid advances in high-throughput sequencing (HTS) technologies which generate relatively short reads resulting in highly fragmented assemblies consisting of contigs. Additional long-range linkage information is typically used to orient, order, and link contigs into larger(More)
The precipitous drop in sequencing costs has generated much enthusiasm for very large scale genome sequenc-ing initiatives. However, assembling high-quality genome sequences from the short reads currently generated by high-throughput sequencing (HTS) technologies represents a formidable computational challenge that has yet to be met. In this work we address(More)
The rapidly diminishing cost of genome sequencing is driving renewed interest in large scale genome sequencing programs such as Genome 10K (G10K). Despite renewed interest the assembly of large genomes from short reads is still an extremely resource intensive process. This work presents a scalable algorithms to create scaffolds, or ordered and oriented sets(More)
The number of sequenced genomes is growing very quickly due to the low cost and availability of high through-put DNA sequencing platforms. However, most genome sequences are not complete, consisting of large numbers of contigs separated by gaps. The process of orienting and ordering these contigs, typically using pairs of reads with approximately known(More)
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