Year: 2014
Type: article
Abstract: In the next generation sequencing techniques millions of short reads are produced from a genomic sequence at a single run. The chances of low read coverage to some regions of the sequence are very high. The reads are short and very large in number. Due to erroneous base calling, there could be errors in the reads. As a consequence, sequence assemblers often fail to sequence an entire DNA molecule and instead output a set of overlapping segments that together represent a consensus region of the DNA. This set of overlapping segments are collectively called contigs in the literature. The final step of the sequencing process, called scaffolding, is to assemble the contigs into a correct order. Scaffolding techniques typically exploit additional information such as mate-pairs, pair-ends, or optical restriction maps. In this paper we introduce a series of novel algorithms for scaffolding that exploit optical restriction maps (ORMs). Simulation results show that our algorithms are indeed reliable, scalable, and efficient compared to the best known algorithms in the literature.
Source: BMC Genomics
Authors: Subrata Saha, Sanguthevar Rajasekaran
Institution: University of Connecticut
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $3,090
OpenAlex ID: W2156406701