DeepSimulator1.5: a more powerful, quicker and lighter simulator for Nanopore sequencing.
KAUST DepartmentBiological and Environmental Sciences and Engineering (BESE) Division
Computational Bioscience Research Center (CBRC)
Computer Science Program
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Structural and Functional Bioinformatics Group
Online Publication Date2020-01-08
Print Publication Date2020-04-15
Permanent link to this recordhttp://hdl.handle.net/10754/661086
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AbstractMOTIVATION:Nanopore sequencing is one of the leading third-generation sequencing technologies. A number of computational tools have been developed to facilitate the processing and analysis of the Nanopore data. Previously, we have developed DeepSimulator1.0 (DS1.0), which is the first simulator for Nanopore sequencing to produce both the raw electrical signals and the reads. However, although DS1.0 can produce high-quality reads, for some sequences, the divergence between the simulated raw signals and the real signals can be large. Furthermore, the Nanopore sequencing technology has evolved greatly since DS1.0 was released. It is thus necessary to update DS1.0 to accommodate those changes. RESULTS:We propose DeepSimulator1.5 (DS1.5), all three modules of which have been updated substantially from DS1.0. As for the sequence generator, we updated the sample read length distribution to reflect the newest real reads' features. In terms of the signal generator, which is the core of DeepSimulator, we added one more pore model, the context-independent pore model, which is much faster than the previous context-dependent one. Furthermore, to make the generated signals more similar to the real ones, we added a low-pass filter to post-process the pore model signals. Regarding the basecaller, we added the support for the newest official basecaller, Guppy, which can support both GPU and CPU. In addition, multiple optimizations, related to multiprocessing control, memory, and storage management, have been implemented to make DS1.5 a much more amenable and lighter simulator than DS1.0. AVAILABILITY:The main program and the data are available at https://github.com/lykaust15/DeepSimulator.
CitationLi, Y., Wang, S., Bi, C., Qiu, Z., Li, M., & Gao, X. (2020). DeepSimulator1.5: a more powerful, quicker and lighter simulator for Nanopore sequencing. Bioinformatics. doi:10.1093/bioinformatics/btz963
SponsorsWe would like to thank all the users that have discussed with us on Github, which have definitely improved DeepSimulator greatly, resulting in DeepSimulator1.5. We want to thank Jia-Xing Yue especially for his constructive feedbacks.
This work was supported by the King Abdullah University of Science and Technology (KAUST), under award number FCC/1/1976-18-01, FCC/1/ 1976-23-01, FCC/1/1976-25-01, FCC/1/1976-26-01, URF/1/3412-01-01, URF/1/3450-01-01 and FCS/1/4102-02-01.
PublisherOxford University Press (OUP)
JournalBioinformatics (Oxford, England)
CollectionsArticles; Biological and Environmental Science and Engineering (BESE) Division; Bioscience Program; Structural and Functional Bioinformatics Group; Computer Science Program; Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Science and Engineering (CEMSE) Division
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