SWAMPy: simulating SARS-CoV-2 wastewater amplicon metagenomes.

ABSTRACT:

Motivation

Tracking SARS-CoV-2 variants through genomic sequencing has been an important part of the global response to the pandemic and remains a useful tool for surveillance of the virus. As well as whole-genome sequencing of clinical samples, this surveillance effort has been aided by amplicon sequencing of wastewater samples, which proved effective in real case studies. Because of its relevance to public healthcare decisions, testing and benchmarking wastewater sequencing analysis methods is also crucial, which necessitates a simulator. Although metagenomic simulators exist, none is fit for the purpose of simulating the metagenomes produced through amplicon sequencing of wastewater.

Results

Our new simulation tool, SWAMPy (Simulating SARS-CoV-2 Wastewater Amplicon Metage

SUBMITTER: Boulton W 

PROVIDER: S-EPMC11401744 | biostudies-literature | 2024 Sep

REPOSITORIES: biostudies-literature