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Credit: Mary Ann Liebert, Inc., publishers
A new study compares and assesses eight de novo genome assembly software tools on actual viral next-generation sequencing data. The study, which includes the whole genome sequence data of SARS-CoV-2, the virus that causes COVID-19, is published in the peer-reviewed OMICS: A Journal of Integrative Biology. Click here to read the article now.
Genome assembly is one of the crucial steps in whole genome sequencing data analyses and understanding viral genomics. A variety of different genome assembly software tools have been developed. In the present study, coauthors Amit Kumar Gupta and Manoj Kumar, from the Institute of Microbial Technology, Council of Scientific and Industrial Research, and the Academy of Scientific and Innovative Research, in India, performed a comparative evaluation and benchmarking of eight assemblers on viral next-generation sequencing data.
The investigators concluded that “overall, three assemblers, i.e., SPAdes, IDBA, and ABySS, performed consistently well, including for genome assembly of SARS-CoV-2.” They also suggest that using two or more assembly approaches should be considered in viral next-generation sequencing studies, especially 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, West Nile virus, amongst others. 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 Vural Özdemir, MD, PhD, DABCP, Editor-in-Chief of OMICS.
About the Journal
OMICS: A Journal of Integrative Biology is an authoritative and highly innovative peer-reviewed interdisciplinary journal published monthly online, addressing the latest advances at the intersection of postgenomics medicine, biotechnology and global society, including the integration of multi-omics knowledge, data analyses and modeling, and applications of high-throughput approaches to study complex biological and societal problems. Public policy, governance and societal aspects of the large-scale biology and 21st century data-enabled sciences are also peer-reviewed. Complete tables of content and a sample issue may be viewed on the OMICS: A Journal of Integrative Biology website.
About the Publisher
Mary Ann Liebert, Inc., publishers is known for establishing authoritative peer-reviewed journals in many areas of science and biomedical research. Its biotechnology trade magazine, Genetic Engineering & Biotechnology News (GEN), was the first in its field and is today the industry’s most widely read publication worldwide. A complete list of the firm’s more than 100 journals, books, and newsmagazines is available on the Mary Ann Liebert, Inc., publishers website.
Method of Research
Observational study
Subject of Research
Not applicable
Article Title
Benchmarking and Assessment of Eight De Novo Genome Assemblers on Viral Next-Generation Sequencing Data, Including the SARS-CoV-2