Mge-cluster: a reference-free approach for typing bacterial plasmids.

ABSTRACT: Extrachromosomal elements of bacterial cells such as plasmids are notorious for their importance in evolution and adaptation to changing ecology. However, high-resolution population-wide analysis of plasmids has only become accessible recently with the advent of scalable long-read sequencing technology. Current typing methods for the classification of plasmids remain limited in their scope which motivated us to develop a computationally efficient approach to simultaneously recognize novel types and classify plasmids into previously identified groups. Here, we introduce mge-cluster that can easily handle thousands of input sequences which are compressed using a unitig representation in a de Bruijn graph. Our approach offers a faster runtime than existing algorithms, with moderate mem

SUBMITTER: Arredondo-Alonso S 

PROVIDER: S-EPMC10331934 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature