Hybrid assembly, using a combination of long and short reads, can achieve complete and accurate genome assemblies of bacterial isolates. However, mistakes often occur in both assembly and polishing algorithms, making error-free genome sequences difficult to obtain. Here we present two new software tools to assist in this pursuit. Trycycler combines multiple long-read assemblies of a single genome into a high-quality consensus assembly. In doing so, it can avoid many of the errors which commonly afflict long-read assemblies. Polypolish uses short reads to correct errors in long-read assemblies. Unlike other short-read polishing tools, it uses a repeat-aware algorithm that allows for the correction of errors in genomic repeats. Together, Trycycler and Polypolish bring perfect assemblies of bacterial genomes within reach.
Research Assistant, Department of Infectious Diseases, Central Clinical School, Monash University
Ryan is a PhD student and research assistant in Kathryn Holt’s lab at Monash University where he works on assembly algorithms for bacterial genomes. He has a particular interest in long-read assembly (especially using Oxford Nanopore reads) and hybrid assembly which combines both short and long reads. He is the developer of Bandage, Unicycler, Porechop, Filtlong and Badread. More recently, he has developed Trycycler and Polypolish, two tools which aim to enable zero-error bacterial genome assemblies.