Researchers have benchmarked software tools for de novo genome assembly after analysing and comparing eight tools and come to a conclusion that SPAdes, IDBA, and ABySS, performed consistently well, including for genome assembly of SARS-CoV-2. Further they also recommend that two or more assembly approaches should be considered in viral next-generation sequencing studies, especially in clinical settings.
Genome assembly is one of the crucial steps in whole genome sequencing data analyses and understanding viral genomics. There are a number of software tools available in the market. 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.
They found three assemblers, SPAdes, IDBA, and ABySS, to be performing well consistently, but they are quick to point out that a single assembly approach might not be ideal in a clinical setting and that use of two or more assembly approaches should be considered in viral next-generation sequencing studies, especially in clinical settings.
For molecular epidemiology and clinical management genome assembly is very critical and it was evident during the pandemic. 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.
The benchmarking of the genome assembly tools is a great example of genomic applications in planetary health and opens up new possibilities to accelerate innovation in clinical diagnostics, drug and vaccine development.