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DeepSimulator1.5: a more powerful, quicker and lighter simulator for Nanopore sequencing
Yu Li1, Sheng Wang1,2, Chongwei Bi3
1Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
Bioinformatics (Oxford, England)
|January 9, 2020
Summary
DeepSimulator1.5 (DS1.5) enhances Nanopore sequencing simulation by improving signal accuracy and computational efficiency. This updated tool provides more realistic raw signal generation and supports the latest basecalling software for advanced bioinformatics analysis.
Area of Science:
- Bioinformatics and Computational Biology
- Genomics and Molecular Biology
- Next-Generation Sequencing Technologies
Background:
- Nanopore sequencing is a leading third-generation sequencing technology.
- Existing computational tools aid in Nanopore data processing and analysis.
- DeepSimulator 1.0 (DS1.0) was the first simulator for Nanopore sequencing, generating raw electrical signals and reads.
Purpose of the Study:
- To address limitations in DeepSimulator 1.0, specifically the divergence between simulated and real signals for certain sequences.
- To update the Nanopore sequencing simulator to accommodate significant advancements in the technology since DS1.0's release.
- To develop DeepSimulator 1.5 (DS1.5) for more accurate and efficient Nanopore data simulation.
Main Methods:
- Updated the sequence generator's read length distribution to match current Nanopore sequencing data.
- Introduced a faster, context-independent pore model and a low-pass filter in the signal generator for improved signal realism.
- Integrated support for the Guppy basecaller (GPU/CPU compatible) and implemented optimizations for multiprocessing, memory, and storage.
Main Results:
- DeepSimulator 1.5 (DS1.5) offers substantial updates to all three core modules compared to DS1.0.
- The new pore model and signal post-processing enhance the similarity between simulated and real Nanopore signals.
- DS1.5 is significantly more amenable and lighter than DS1.0 due to implemented optimizations.
Conclusions:
- DS1.5 provides a more accurate and efficient simulation of Nanopore sequencing data, reflecting technological advancements.
- The enhanced simulation capabilities of DS1.5 will benefit the processing and analysis of Nanopore sequencing data in bioinformatics.
- The updated simulator is available for use by the research community.
