PipeCoV: a pipeline for the assembly, annotation and identification of SARS-CoV-2 genome variants

This article was originally published here

Peer J. 2022 Apr 13;10:e13300. doi: 10.7717/peerj.13300. eCollection 2022.

ABSTRACT

MOTIVATION: Since the identification of the new coronavirus (SARS-CoV-2), the scientific community has made a huge effort to understand the biology of the virus and to develop vaccines. Next-generation sequencing strategies have provided insight into the evolution of infectious diseases and facilitated the development of molecular diagnostics and treatments. Thousands of genomes are generated every week to understand the genetic characteristics of this virus. Efficient pipelines are needed to analyze the large amount of data generated. Here we present a novel pipeline designed for genomic analysis and identification of SARS-CoV-2 virus variants.

RESULTS: PipeCoV shows better performance compared to well-established SARS-CoV-2 pipelines, with lower Ns content and higher genomic coverage compared to the Wuhan reference. It also provides a variant report not offered by other tested pipelines.

AVAILABILITY: https://github.com/alvesrco/pipecov.

PMID:35437474 | CPM:PMC9013232 | DO I:10.7717/peerj.13300