SWAMPy: simulating SARS-CoV-2 wastewater amplicon metagenomes

• Published in: Bioinformatics (Oxford, England) Vol. 40; no. 9
• Main Authors: Boulton, William, Fidan, Fatma Rabia, Denise, Hubert, De Maio, Nicola, Goldman, Nick
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 02.09.2024; Oxford Publishing Limited (England)
• Subjects: Availability; COVID-19; Gene sequencing; Metagenomics; Pandemics; Severe acute respiratory syndrome coronavirus 2; Simulators; Surveillance; Viral diseases; Wastewater; Water sampling; Whole genome sequencing
• ISSN: 1367-4811; 1367-4803; 1367-4811
• DOI: 10.1093/bioinformatics/btae532

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 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. Availability and implementation The code for this project is available at https://github.com/goldman-gp-ebi/SWAMPy. It can be installed on any Unix-based operating system and is available under the GPL-v3 license.