SOPRA: Scaffolding algorithm for paired reads via statistical optimization

Background: High throughput sequencing (HTS) platforms produce gigabases of short read (<100 bp) data per run. While these short reads are adequate for resequencing applications, de novo assembly of moderate size genomes from such reads remains a significant challenge. These limitations could be partially overcome by utilizing mate pair technology, which provides pairs of short reads separated by a known distance along the genome. Results: We have developed SOPRA, a tool designed to exploit the mate pair/paired-end information for assembly of short reads. The main focus of the algorithm is selecting a sufficiently large subset of simultaneously satisfiable mate pair constraints to achieve a balance between the size and the quality of the output scaffolds. Scaffold assembly is presented as an optimization problem for variables associated with vertices and with edges of the contig connectivity graph. Vertices of this graph are individual contigs with edges drawn between contigs conne...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Adel Dayarian, Todd P. Michael, Anirvan M. Sengupta
• Keywords: BMCBI 2010, Mate Pair Technology, Mate Pairs, Short Reads