PipeCoV: a pipeline for SARS-CoV-2 genome assembly, annotation and variant identification

PeerJ

article

Renato R. M. Oliveira¹  Tatianne Costa Negri¹  Gisele Nunes¹  Inácio Medeiros³  Guilherme Araújo³  Fabricio de Oliveira Silva¹  Jorge Estefano Santana de Souza³  Ronnie Alves¹  Guilherme Oliveira¹ 

[1] Environmental Genomics, Instituto Tecnológico Vale;Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais;Programa de Pós-Graduação em Bioinformática, Universidade Federal do Rio Grande do Norte;Bioinformatics Multidisciplinary Environment, Universidade Federal do Rio Grande do Norte;Programa de Pós-Graduação em Ciência da Computação, Universidade Federal do Pará

关键词: Sarscov2;    Genomics;    Variant identification;    Covid19;    Pipeline;    Annotation;    Virus;   

DOI  :  10.7717/peerj.13300

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

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.

【 授权许可】

CC BY