StrainXpress: strain aware metagenome assembly from short reads.

ABSTRACT: Next-generation sequencing-based metagenomics has enabled to identify microorganisms in characteristic habitats without the need for lengthy cultivation. Importantly, clinically relevant phenomena such as resistance to medication, virulence or interactions with the environment can vary already within species. Therefore, a major current challenge is to reconstruct individual genomes from the sequencing reads at the level of strains, and not just the level of species. However, strains of one species can differ only by minor amounts of variants, which makes it difficult to distinguish them. Despite considerable recent progress, related approaches have remained fragmentary so far. Here, we present StrainXpress, as a comprehensive solution to the problem of strain aware metagenome assembly from

SUBMITTER: Kang X 

PROVIDER: S-EPMC9508831 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature