De novo finished 2.8 Mbp Staphylococcus aureus genome assembly from 100 bp short and long range paired-end reads

Paired-end sequencing allows circumventing the shortness of the reads produced by second generation sequencers and is essential for de novo assembly of genomes. However, obtaining a finished genome from short reads is still an open challenge. We present an algorithm that exploits the pairing information issued from inserts of potentially any length. The method determines paths through an overlaps graph by using a constrained search tree. We also present a method that automatically determines suited overlaps cutoffs according to the contextual coverage, reducing thus the need for manual parameterization. Finally, we introduce an interactive mode that allows querying an assembly at targeted regions.