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.

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To tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS), most of the existing short-read aligners can be configured to favor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveraging the computational power of both CPU and GPU with optimized algorithms, delivers high speed and sensitivity simultaneously. Compared with widely adopted aligners including BWA, Bowtie2, SeqAlto, CUSHAW2, GEM and GPU-based aligners BarraCUDA and CUSHAW, SOAP3-dp was found to be two to tens of times faster, while maintaining the highest sensitivity and lowest false discovery rate (FDR) on Illumina reads with different lengths. Transcending its predecessor SOAP3, which does not allow gapped alignment, SOAP3-dp by default tolerates alignment similarity as low as 60%. Real data evaluation using human genome demonstrates SOAP3-dp's power to enable more authentic variants and longer Indels to be discovered. Fosmid sequencing shows a 9.1% FDR on newly discovered deletions. SOAP3-dp natively supports BAM file format and provides the same scoring scheme as BWA, which enables it to be integrated into existing analysis pipelines. SOAP3-dp has been deployed on Amazon-EC2, NIH-Biowulf and Tianhe-1A.

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 could unveil important information to the data analyst. Existing approaches for discovering periodic patterns focus on symbol sequences. However, these methods cannot directly be applied to a spatiotemporal sequence because of the fuzziness of spatial locations in the sequence. In this paper, we define the problem of mining periodic patterns in spatiotemporal data and propose an effective and efficient algorithm for retrieving maximal periodic patterns. In addition, we study two interesting variants of the problem. The first is the retrieval of periodic patterns that are frequent only during a continuous subinterval of the whole history. The second problem is the discovery of periodic patterns, whose instances may be shifted or distorted. We demonstrate how our mining technique can be adapted for these variants. Finally, we present a comprehensive experimental evaluation, where we show the effectiveness and efficiency of the proposed techniques.