Crykey: Rapid Identification of SARS-CoV-2 Cryptic Mutations in Wastewater.

ABSTRACT: We present Crykey, a computational tool for rapidly identifying cryptic mutations of SARS-CoV-2. Specifically, we identify co-occurring single nucleotide mutations on the same sequencing read, called linked-read mutations, that are rare or entirely missing in existing databases, and have the potential to represent novel cryptic lineages found in wastewater. While previous approaches exist for identifying cryptic linked-read mutations from specific regions of the SARS-CoV-2 genome, there is a need for computational tools capable of efficiently tracking cryptic mutations across the entire genome and for tens of thousands of samples and with increased scrutiny, given their potential to represent either artifacts or hidden SARS-CoV-2 lineages. Crykey fills this gap by identifying rare linked-r

SUBMITTER: Liu Y 

PROVIDER: S-EPMC10659477 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature