Study evaluates eight de novo genome assembly software tools on next-generation viral sequencing data

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A new study compares and evaluates eight de novo genome assembly software tools on real next-generation viral sequencing data. The study, which includes the full genome sequence data of SARS-CoV-2, the virus that causes COVID-19, is published in the peer-reviewed journal OMICS: a journal of integrative biology.

Genome assembly is one of the crucial steps in analyzing whole genome sequencing data and understanding viral genomics. A variety of different genome assembly software tools have been developed. In the present study, co-authors Amit Kumar Gupta and Manoj Kumar, Institute of Microbial Technology, Council for Scientific and Industrial Research, and Academy of Scientific and Innovative Research, India, conducted a comparative assessment and a comparative analysis of eight assemblers on virus next-generation sequencing data.

Investigators concluded that “overall, three assemblers, i.e., SPAdes, IDBA, and ABySS, consistently performed well, including for SARS-CoV-2 genome assembly.” They also suggest that the use of two or more assembly approaches should be considered in next-generation viral sequencing studies, especially in clinical settings.

Genome assembly is critical to the molecular epidemiology and clinical management of COVID-19 and other infectious outbreaks. Benchmarking of genome assembly tools has been lacking on viral-derived data. The new study fills this knowledge gap, drawing on sequencing data from SARS-CoV-2, dengue virus 3, human immunodeficiency virus 1, hepatitis B virus, West Nile virus, among others. This benchmarking is a great example of genomics applications in planetary health and opens new possibilities to accelerate innovation in clinical diagnostics, drug and vaccine development. I welcome new manuscripts dealing with large-scale research in multi-omics biology and ecology for peer review in the journal.


Vural Ozdemir, MD, PhD, DABCP, Editor-in-Chief of OMIC

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Journal reference:

Gupta, AK and Kumar, M., (2022) Comparative analysis and evaluation of eight de novo genome assemblers on next-generation viral sequencing data including SARS-CoV-2. OMICS: a journal of integrative biology. doi.org/10.1089/omi.2022.0042.

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