SWAMPy: simulating SARS-CoV-2 wastewater amplicon metagenomes

Boulton W., Fidan F. R., Denise H., De Maio N., Goldman N.

Bioinformatics, vol.40, no.9, 2024 (SCI-Expanded) identifier identifier identifier

  • Publication Type: Article / Article
  • Volume: 40 Issue: 9
  • Publication Date: 2024
  • Doi Number: 10.1093/bioinformatics/btae532
  • Journal Name: Bioinformatics
  • Journal Indexes: Science Citation Index Expanded (SCI-EXPANDED), Scopus, Academic Search Premier, Aerospace Database, Applied Science & Technology Source, BIOSIS, Biotechnology Research Abstracts, CAB Abstracts, Communication Abstracts, Computer & Applied Sciences, EMBASE, INSPEC, MEDLINE, Metadex, Veterinary Science Database, Civil Engineering Abstracts
  • Middle East Technical University Affiliated: Yes

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.