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Alosaimi S, Bandiang A, van Biljon N, Awany D, Thami PK, Tchamga MSS, Kiran A, Messaoud O, Hassan RIM, Mugo J, Ahmed A, Bope CD, Allali I, Mazandu GK, Mulder NJ, Chimusa ER. A broad survey of DNA sequence data simulation tools. Brief Funct Genomics 2020; 19:49-59. [PMID: 31867604 DOI: 10.1093/bfgp/elz033] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 10/27/2019] [Accepted: 11/04/2019] [Indexed: 11/12/2022] Open
Abstract
In silico DNA sequence generation is a powerful technology to evaluate and validate bioinformatics tools, and accordingly more than 35 DNA sequence simulation tools have been developed. With such a diverse array of tools to choose from, an important question is: Which tool should be used for a desired outcome? This question is largely unanswered as documentation for many of these DNA simulation tools is sparse. To address this, we performed a review of DNA sequence simulation tools developed to date and evaluated 20 state-of-art DNA sequence simulation tools on their ability to produce accurate reads based on their implemented sequence error model. We provide a succinct description of each tool and suggest which tool is most appropriate for the given different scenarios. Given the multitude of similar yet non-identical tools, researchers can use this review as a guide to inform their choice of DNA sequence simulation tool. This paves the way towards assessing existing tools in a unified framework, as well as enabling different simulation scenario analysis within the same framework.
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Affiliation(s)
- Shatha Alosaimi
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Armand Bandiang
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Noelle van Biljon
- Computational Biology Division, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Denis Awany
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Prisca K Thami
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Milaine S S Tchamga
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Anmol Kiran
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi.,Edinburgh University, Edinburgh, UK
| | - Olfa Messaoud
- Université de Tunis El Manar, Institut Pasteur de Tunis, LR16IPT05 Génomique Biomédicale et Oncogénétique, Tunis, 1002, Tunisia
| | - Radia Ismaeel Mohammed Hassan
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Jacquiline Mugo
- Computational Biology Division, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Azza Ahmed
- Centre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum, Sudan
| | - Christian D Bope
- Computational Biology Division, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Imane Allali
- Computational Biology Division, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Gaston K Mazandu
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Computational Biology Division, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,African Institute for Mathematical Sciences (AIMS), Cape Town, South Africa
| | - Nicola J Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Emile R Chimusa
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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