Background: There 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. Findings: To 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. Conclusions: Benchmark 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.

We have developed a new method, SOAPfuse, to identify fusion transcripts from paired-end RNA-Seq data. SOAPfuse applies an improved partial exhaustion algorithm to construct a library of fusion junction sequences, which can be used to efficiently identify fusion events, and employs a series of filters to nominate high-confidence fusion transcripts. Compared with other released tools, SOAPfuse achieves higher detection efficiency and consumed less computing resources. We applied SOAPfuse to RNA-Seq data from two bladder cancer cell lines, and confirmed 15 fusion transcripts, including several novel events common to both cell lines. SOAPfuse is available at http://soap.genomics.org.cn/soapfuse.html.

In this paper, a novel signal detector based on matrix information geometric dimensionality reduction (DR) is proposed, which is inspired from spectrogram processing. By short time Fourier transform (STFT), the received data are represented as a 2-D high-precision spectrogram, from which we can well judge whether the signal exists. Previous similar studies extracted insufficient information from these spectrograms, resulting in unsatisfactory detection performance especially for complex signal detection task at low signal-noise-ratio (SNR). To this end, we use a global descriptor to extract abundant features, then exploit the advantages of matrix information geometry technique by constructing the high-dimensional features as symmetric positive definite (SPD) matrices. In this case, our task for signal detection becomes a binary classification problem lying on an SPD manifold. Promoting the discrimination of heterogeneous samples through information geometric DR technique that is dedicated to SPD manifold, our proposed detector achieves satisfactory signal detection performance in low SNR cases using the K distribution simulation and the real-life sea clutter data, which can be widely used in the field of signal detection.

Traditionally, Rayleigh scattering is thought to only impact fiber sensing system performance when the leading fiber is over 10 km long. However, this report illustrates theoretically and experimentally that Rayleigh scattering cannot be ignored in fiber optic interferometric sensor (FOIS) even with several hundred‐meter common leading fiber because of the interaction of Rayleigh backward scattering (RBS) and returning interference signal. Herein, a conceptual framework is developed to elucidate the interaction between RBS and FOIS interference, revealing that, beyond laser monochromacity, the self‐correction characteristic of laser pulses also influences coherent superposition. Building upon this novel insight, a phase modulation method based on pseudorandom noise (PRN) code is first proposed to address coherent RBS stacking on returning FOIS interferences while preserving high laser monochromacity. By modulating the interrogation pulses, a 21.3 dB suppression of background phase noise is achieved in FOIS with 3.3 km leading fiber. This study offers a holistic understanding of Rayleigh scattering in the leading fiber, encompassing experimental observations, theoretical modeling, physics analysis, and its resolution, thereby contributing to advancements in underwater sensing to broaden the understanding of the underwater environment.

Internal solitary waves are very common physical phenomena in the ocean, which play an important role in the transport of marine matter, momentum and energy. Because the generalized nonlinear Schrödinger equation can well explain the effects of nonlinearity and dispersion in the ocean, it is more suitable for describing the deep-sea internal wave propagation and evolution than other mathematical models. At first, by designing skillfully the trial-Lagrange functional, different kinds of variational principles are successfully established for a generalized nonlinear Schrödinger equation by the semi-inverse method. Then, the constructed variational principles are proved correct by minimizing the functionals with the calculus of variations. Furthermore, some kinds of internal solitary wave solutions are obtained and demonstrated by semi-inverse variational principle for the generalized nonlinear Schrödinger equation.