A broad survey of DNA sequence data simulation tools

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 desir...

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Bibliographic Details
Published in:Briefings in functional genomics 2020-01, Vol.19 (1), p.49-59
Main Authors: Alosaimi, Shatha, Bandiang, Armand, van Biljon, Noelle, Awany, Denis, Thami, Prisca K, Tchamga, Milaine S S, Kiran, Anmol, Messaoud, Olfa, Hassan, Radia Ismaeel Mohammed, Mugo, Jacquiline, Ahmed, Azza, Bope, Christian D, Allali, Imane, Mazandu, Gaston K, Mulder, Nicola J, Chimusa, Emile R
Format: Article
Language:English
Subjects:
Computer Simulation
DNA - analysis
DNA - genetics
Genome, Human
Genomics - methods
High-Throughput Nucleotide Sequencing
Humans
Review Paper
Sequence Analysis, DNA - methods
Software
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Summary: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.
ISSN:2041-2657
2041-2649
2041-2657
DOI:10.1093/bfgp/elz033