Background: Metagenomic assembly is a challenging problem due to the presence of genetic material from multiple organisms. The problem becomes even more difficult when short reads produced by next generation sequencin...
详细信息
ISBN:
(纸本)9781424483075
Background: Metagenomic assembly is a challenging problem due to the presence of genetic material from multiple organisms. The problem becomes even more difficult when short reads produced by next generation sequencing technologies are used. Although whole genome assemblers are not designed to assemble metagenomic samples, they are being used for metagenomics due to the lack of assemblers capable of dealing with metagenomic samples. We present an evaluation of assembly of simulated short-read metagenomic samples using a state-of-art de Bruijn graph based assembler. Results: We assembled simulated metagenomic reads from datasets of various complexities using a state-of-art de Bruijn graph based parallel assembler. We have also studied the effect of k-mer size used in de Bruijn graph on metagenomic assembly and developed a clustering solution to pool the contigs obtained from different assembly runs, which allowed us to obtain longer contigs. We have also assessed the degree of chimericity of the assembled contigs using an entropy/impurity metric and compared the metagenomic assemblies to assemblies of isolated individual source genomes. Conclusions: Our results show that accuracy of the assembled contigs was better than expected for the metagenomic samples with a few dominant organisms and was especially poor in samples containing many closely related strains. Clustering contigs from different k-mer parameter of the de Bruijn graph allowed us to obtain longer contigs, however the clustering resulted in accumulation of erroneous contigs thus increasing the error rate in clustered contigs.
Background: Genome assembly is considered to be a challenging problem in computational biology, and has been studied extensively by many researchers. It is extremely difficult to build a general assembler that is able...
详细信息
In recent years, X-rays and computed tomography (CT) are used today to evaluate bone fractures, with the 3D models extracted from the CT images,(1) the dislocation and displacement of bone fragments computed by an ass...
详细信息
ISBN:
(数字)9781510679931
ISBN:
(纸本)9781510679931;9781510679924
In recent years, X-rays and computed tomography (CT) are used today to evaluate bone fractures, with the 3D models extracted from the CT images,(1) the dislocation and displacement of bone fragments computed by an assembly simulation using 3D models are necessary for a successful surgical treatment. This paper proposes a method to assemble the point cloud data of the simple fractured bone fragments. Using a multi-layered segmentation method to merge the bone surface, the initial position of the point cloud data is obtained to improve the accuracy of the ICP method.
Background: Physical mapping of DNA with restriction enzymes allows for the characterization and assembly of much longer molecules than is feasible with sequencing. However, assemblies of physical map data are sensiti...
详细信息
Background: Physical mapping of DNA with restriction enzymes allows for the characterization and assembly of much longer molecules than is feasible with sequencing. However, assemblies of physical map data are sensitive to input parameters, which describe noise inherent in the data collection process. One possible way to determine the parameter values that best describe a dataset is by trial and error. Results: Here we present OMWare, a tool that efficiently generated 405 de novo map assemblies of a single datasets collected from the cotton species Gossypium raimondii. The assemblies were generated using various input parameter values, and were completed more efficiently by re-using compatible intermediate results. These assemblies were assayed for contiguity, internal consistency, and accuracy. Conclusions: Resulting assemblies had variable qualities. Although highly accurate assemblies were found, contiguity and internal consistency metrics were poor predictors of accuracy.
On-board switching has been the development trend of satellite communication. There is electronic bottleneck in the development of on-board ATM switch, so the optical switch is the inevitable direction of future broad...
详细信息
ISBN:
(纸本)9781849195072
On-board switching has been the development trend of satellite communication. There is electronic bottleneck in the development of on-board ATM switch, so the optical switch is the inevitable direction of future broadband multimedia satellite. The paper brings forward a scheme about on-board mixed optical/electronic switching of GEO, analyses the switching mode of the scheme, discusses the key techniques.
Hybrid optical switching (HOS) combines the advantages of optical circuit switching (OCS) and optical burst switching (OBS). But HOS can not dynamically change the optical switching paradigm according to the traffic f...
详细信息
ISBN:
(纸本)9780819469465
Hybrid optical switching (HOS) combines the advantages of optical circuit switching (OCS) and optical burst switching (OBS). But HOS can not dynamically change the optical switching paradigm according to the traffic fluctuation. it can not efficiently support burst traffic. And the utilization of some lightpath in HOS networks is low. To solve the problems, a self-adaptive hybrid optical switching (S-HOS) is proposed in the paper. In S-HOS networks, ingress edge nodes monitor the traffic between a pair of an ingress node and an egress node, and based on the monitor results edge nodes self-adaptively adjust optical switching paradigm. Based on minimum burst length maximum assembly period algorithm, a new assembly algorithm of S-HOS is proposed to improve the lightpath utilization and efficiently support burst IP traffic. And a data channel scheduling is proposed to assign data channel resources for the lightpaths and data bursts by regarding lightpath as a huge data burst. And it can decrease the complexity of hybrid optical switching and improve the network performance. Simulation results show that S-HOS outperforms OBS in term of IP packet dropping probability and end-to-end delay.
We present a framework for the design of optimal assembly algorithms for shotgun sequencing under the criterion of complete reconstruction. We derive a lower bound on the read length and the coverage depth required fo...
详细信息
We present a framework for the design of optimal assembly algorithms for shotgun sequencing under the criterion of complete reconstruction. We derive a lower bound on the read length and the coverage depth required for reconstruction in terms of the repeat statistics of the genome. Building on earlier works, we design a de Brujin graph based assembly algorithm which can achieve very close to the lower bound for repeat statistics of a wide range of sequenced genomes, including the GAGE datasets. The results are based on a set of necessary and sufficient conditions on the DNA sequence and the reads for reconstruction. The conditions can be viewed as the shotgun sequencing analogue of Ukkonen-Pevzner's necessary and sufficient conditions for Sequencing by Hybridization.
暂无评论