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Updated: Sep 26, 2025

Quantification and Whole Genome Characterization of SARS-CoV-2 RNA in Wastewater and Air Samples
Published on: June 30, 2023
PipeCoV: a pipeline for SARS-CoV-2 genome assembly, annotation and variant identification
Renato R M Oliveira1,2, Tatianne Costa Negri1, Gisele Nunes1
1Environmental Genomics, Instituto Tecnológico Vale, Belém, Pará, Brazil.
Motivation:
Since the identification of the novel coronavirus (SARS-CoV-2), the scientific community has made a huge effort to understand the virus biology and to develop vaccines. Next-generation sequencing strategies have been successful in understanding the evolution of infectious diseases as well as facilitating the development of molecular diagnostics and treatments. Thousands of genomes are being generated weekly to understand the genetic characteristics of this virus. Efficient pipelines are needed to analyze the vast amount of data generated. Here we present a new pipeline designed for genomic analysis and variant identification of the SARS-CoV-2 virus.
Results:
PipeCoV shows better performance when compared to well-established SARS-CoV-2 pipelines, with a lower content of Ns and higher genome coverage when compared to the Wuhan reference. It also provides a variant report not offered by other tested pipelines.
Availability:
https://github.com/alvesrco/pipecov.
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