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Credit: Mary Ann Liebert, Inc., publishers
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 OMIC: A Journal of Integrative Biology. Click here to read the article now.
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 this study, the co-authors Amit Kumar Gupta and Manoj Kumarfrom the Institute of Microbial Technology, Council of Scientific and Industrial Research and Academy of Scientific and Innovative Research, India, conducted benchmarking and benchmarking of eight assemblers on viral sequencing data from new generation.
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 vital for 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,” said Vural Ozdemir, MD, PhD, DABCP, Chief Editor of OMIC.
About the journal
OMICS: a journal of integrative biology is an authoritative and highly innovative peer-reviewed interdisciplinary journal published online monthly, covering the latest advances at the intersection of post-genomic medicine, biotechnology and global society, including the integration of multi -omics, data analysis and modeling, and applications of high-throughput approaches to study complex biological and societal problems. Public policy, governance and societal aspects of large-scale biology and 21st century data-driven science are also peer-reviewed. Full tables of contents and sample issue can be viewed on the OMICS: a journal of integrative biology website.
About the editor
Mary Ann Liebert, Inc., publishers is known for establishing authoritative, peer-reviewed journals in many areas of science and biomedical research. Its professional biotechnology magazine, Genetic Engineering and Biotechnology News (GEN), was the first in its field and is today the most widely read industry publication in the world. A complete listing of the firm’s more than 100 journals, books and newsmagazines is available at Mary Ann Liebert, Inc., publishers website.
Research method
Observational study
Research subject
Not applicable
The title of the article
Comparative analysis and evaluation of eight de novo genome assemblers on next-generation viral sequencing data, including SARS-CoV-2
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