PipeCoV: a pipeline for SARS-CoV-2 genome assembly, annotation and variant identification.
Renato R M Oliveira, Tatianne Costa Negri, Gisele Nunes, In��cio Medeiros, Guilherme Ara��jo, Fabricio de Oliveira Silva, Jorge Estefano Santana de Souza, Ronnie Alves, Guilherme Oliveira
Author Information
Renato R M Oliveira: Environmental Genomics, Instituto Tecnol��gico Vale, Bel��m, Par��, Brazil. ORCID
Tatianne Costa Negri: Environmental Genomics, Instituto Tecnol��gico Vale, Bel��m, Par��, Brazil.
Gisele Nunes: Environmental Genomics, Instituto Tecnol��gico Vale, Bel��m, Par��, Brazil.
In��cio Medeiros: Programa de P��s-Gradua����o em Bioinform��tica, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil.
Guilherme Ara��jo: Programa de P��s-Gradua����o em Bioinform��tica, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil.
Fabricio de Oliveira Silva: Environmental Genomics, Instituto Tecnol��gico Vale, Bel��m, Par��, Brazil.
Jorge Estefano Santana de Souza: Programa de P��s-Gradua����o em Bioinform��tica, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil.
Ronnie Alves: Environmental Genomics, Instituto Tecnol��gico Vale, Bel��m, Par��, 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.
