CoronaSPAdes: from biosynthetic gene clusters to coronaviral assemblies

Abstract

COVID-19 pandemy has ignited a broad scientific interest in coronavirus research. The identification of coronaviridae species in natural reservoirs often requires de novo assembly. However, existing transcriptome assemblers often are not able to assemble coronaviruses into a single contig. We developed coronaSPAdes, a new module for SPAdes assembler for coronavirus species recovery. coronaSPAdes uses the knowledge about coronaviridae genome structure to improve assembly. We have shown that coronaSPAdes outperforms existing SPAdes modes and other popular short-read assemblers in the recovery of full-length coronavirus genomes. This should allow to better understand the coronaviridae spread and diversity.