Accurate hybrid plasmids assembly with HyPlAs

The increasing availability of hybrid sequencing datasets comprising both short and long reads, is radically transforming microbial genomics, with the prospect of obtaining routinely near-complete bacterial genome assemblies. However, the complete assemblies of mobile genetic elements, especially plasmids, still remain challenging. We introduce HyPlAs, an assembly pipeline specifically designed to assemble plasmids from hybrid bacterial sequencing datasets. HyPlAs main novelty is to incorporate the use of a prior classification of short-read contigs as chromosomal or plasmidic. We evaluate HyPlAs on a large set of bacterial samples and demonstrate that it outperforms its competitor Plassembler. Availability. HyPlAs is freely available at https://github.com/cchauve/HyPlAs.