Clinically relevant RNA-virus whole genome assembly testing on metatranscriptomic data gained directly from COVID-19 clinical samples


Recent pandemics of COVID-19 showed importance of modern methods of molecular biology and bioinformatics in understanding and dealing with such events. In our project, we were sequencing nasopharyngeal swabs from COVID-19 patients. Here in this study, which is a part of mentioned bigger project, we bring brief report of testing RNA virus assembly possibilities for short read Illumina sequencing. We were dealing with metatranscriptomic data from COVID-19 positive patients. There are multiple options of assemblers for RNA genomes. We tested performance of multiple strategies of genome assembly by SPAdes and Trinity. We were evaluating and comparing quality of assemblies with help of Quast tool. We observed, that outcome of assembly is affected by chosen strategy, but we were able to construct genomes only from our short-read sequencing even de novo without using reference genome. Additionally, we assigned assembled genomes to SARS-CoV-2 lineage.

Keywords: RNA virus genome assembly, SPAdes, Trinity, SARS-CoV-2, RNA-seq