BackgroundThere is a rapidly increasing amount of de novo genome assembly using next-generation sequencing (NGS) short reads; however, several big challenges remain to be overcome in order for this to be efficient and accurate. SOAPdenovo has been successfully applied to assemble many published genomes, but it still needs improvement in continuity, accuracy and coverage, especially in repeat regions.FindingsTo overcome these challenges, we have developed its successor, SOAPdenovo2, which has the advantage of a new algorithm design that reduces memory consumption in graph construction, resolves more repeat regions in contig assembly, increases coverage and length in scaffold construction, improves gap closing, and optimizes for large genome.ConclusionsBenchmark using the Assemblathon1 and GAGE datasets showed that SOAPdenovo2 greatly surpasses its predecessor SOAPdenovo and is competitive to other assemblers on both assembly length and accuracy. We also provide an updated assembly version of the 2008 Asian (YH) genome using SOAPdenovo2. Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp, respectively, which is 3-fold and 50-fold longer than the first published version. The genome coverage increased from 81.16% to 93.91%, and memory consumption was ~2/3 lower during the point of largest memory consumption.

Service providers like Google and Amazon are moving into the SaaS (Software as a Service) business. They turn their huge infrastructure into a cloud-computing environment and aggressively recruit businesses to run applications on their platforms. To enforce security and privacy on such a service model, we need to protect the data running on the platform. Unfortunately, traditional encryption methods that aim at providing "unbreakable" protection are often not adequate because they do not support the execution of applications such as database queries on the encrypted data. In this paper we discuss the general problem of secure computation on an encrypted database and propose a SCONEDB (Secure Computation ON an Encrypted DataBase) model, which captures the execution and security requirements. As a case study, we focus on the problem of k-nearest neighbor (kNN) computation on an encrypted database. We develop a new asymmetric scalar-product-preserving encryption (ASPE) that preserves a special type of scalar product. We use APSE to construct two secure schemes that support kNN computation on encrypted data; each of these schemes is shown to resist practical attacks of a different background knowledge level, at a different overhead cost. Extensive performance studies are carried out to evaluate the overhead and the efficiency of the schemes.

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In many applications that track and analyze spatiotemporal data, movements obey periodic patterns; the objects follow the same routes (approximately) over regular time intervals. For example, people wake up at the same time and follow more or less the same route to their work everyday. The discovery of hidden periodic patterns in spatiotemporal data, apart from unveiling important information to the data analyst, can facilitate data management substantially. Based on this observation, we propose a framework that analyzes, manages, and queries object movements that follow such patterns. We define the spatiotemporal periodic pattern mining problem and propose an effective and fast mining algorithm for retrieving maximal periodic patterns. We also devise a novel, specialized index structure that can benefit from the discovered patterns to support more efficient execution of spatiotemporal queries. We evaluate our methods experimentally using datasets with object trajectories that exhibit periodicity.