On actual viral next-generation sequencing data, a recent study compares and evaluates eight de novo genome assembly software tools. The research, which includes the entire genome sequence data of SARS-CoV-2, the virus that causes COVID-19, has been published in the peer-reviewed journal OMICS: A Journal of Integrative Biology.
One of the most important steps in whole genome sequencing data analysis and understanding viral genomics is genome assembly. A wide range of genome assembly software techniques has been developed.
Coauthors Amit Kumar Gupta and Manoj Kumar from India’s Institute of Microbial Technology, Council of Scientific and Industrial Research, and Academy of Scientific and Innovative Research conducted a comparative assessment and performance analysis of eight assemblers on viral next-generation sequencing data in the current study.
The researchers concluded that “overall, three assemblers, i.e., SPAdes, IDBA, and ABySS, performed consistently well, including for genome assembly of SARS-CoV-2.” They also recommend that two or more assembly strategies be used in viral next-generation sequencing research, particularly in clinical settings.
Genome assembly is vital to molecular epidemiology and clinical management of COVID-19 and other infectious outbreaks. Comparative evaluation of the genome assembly tools has been lacking on data from viral origin. The new study fills this knowledge gap, building on sequencing data of SARS-CoV-2, dengue virus 3, human immunodeficiency virus 1, hepatitis B virus, and West Nile virus, amongst others.”
Vural Özdemir, MD, PhD, DABCP, Editor-in-Chief, OMICS
“This benchmarking is a fine example of genomic applications in planetary health and opens up new possibilities to accelerate innovation in clinical diagnostics, drug and vaccine development. I welcome new manuscripts dealing with large-scale biology and multi-omics ecology research for peer-review in the journal,” says Özdemir.
Gupta, A. K., & Kumar, M. (2022) Benchmarking Eight Software Tools for de novo Genome Assembly, Including for SARS-CoV-2. OMICS: A Journal of Integrative Biology. doi.org/10.1089/omi.2022.0042.