Choice of assemblers has a critical impact on de novo assembly of SARS-CoV-2 genome and characterizing variants

Abstract Background Coronavirus Disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a global pandemic following its initial emergence in China. Using next-generation sequencing technologies, a large number of SARS-CoV-2 genomes are being sequenced at an unprecedented rate and being deposited in public repositories. For the de novo assembly of the SARS-CoV-2 genomes, a myriad of assemblers is being used, although their impact on the assembly quality has not been characterized for this virus. In this study, we aim to understand the variabilities on assembly qualities due to the choice of the assemblers. Results We performed 6,648 de novo assemblies of 416 SARS-CoV-2 samples using 8 different assemblers with different k-mers. We used Illumina paired-end…