SWAMPy: simulating SARS-CoV-2 wastewater amplicon metagenomes

Date

2024-09-01

Author

Boulton, William
Fidan, Fatma Rabia
Denise, Hubert
De Maio, Nicola
Goldman, Nick

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This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

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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 Metagenomes with Python), is intended to provide realistic simulated SARS-CoV-2 wastewater sequencing datasets with which other programs that rely on this type of data can be evaluated and improved. Our tool is suitable for simulating Illumina short-read RT-PCR amplified metagenomes.

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https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85204042509&origin=inward
https://hdl.handle.net/11511/111175

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Department of Biology, Article