poreCov-An Easy to Use, Fast, and Robust Workflow for SARS-CoV-2 Genome Reconstruction via Nanopore Sequencing

In response to the SARS-CoV-2 pandemic, a highly increased sequencing effort has been established worldwide to track and trace ongoing viral evolution. Technologies, such as nanopore sequencing the ARTIC protocol are used to reliably generate genomes from raw sequencing data as a crucial base for mo...

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Bibliographic Details
Published in:Frontiers in genetics 2021-07, Vol.12, p.711437-711437
Main Authors: Brandt, Christian, Krautwurst, Sebastian, Spott, Riccardo, Lohde, Mara, Jundzill, Mateusz, Marquet, Mike, Hölzer, Martin
Format: Article
Language:English
Subjects:
bioinformatics
coronavirus – COVID-19
docker
Genetics
lineages
Nextflow
SARS-CoV-2
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Summary:In response to the SARS-CoV-2 pandemic, a highly increased sequencing effort has been established worldwide to track and trace ongoing viral evolution. Technologies, such as nanopore sequencing the ARTIC protocol are used to reliably generate genomes from raw sequencing data as a crucial base for molecular surveillance. However, for many labs that perform SARS-CoV-2 sequencing, bioinformatics is still a major bottleneck, especially if hundreds of samples need to be processed in a recurring fashion. Pipelines developed for short-read data cannot be applied to nanopore data. Therefore, specific long-read tools and parameter settings need to be orchestrated to enable accurate genotyping and robust reference-based genome reconstruction of SARS-CoV-2 genomes from nanopore data. Here we present poreCov, a highly parallel workflow written in Nextflow, using containers to wrap all the tools necessary for a routine SARS-CoV-2 sequencing lab into one program. The ease of installation, combined with concise summary reports that clearly highlight all relevant information, enables rapid and reliable analysis of hundreds of SARS-CoV-2 raw sequence data sets or genomes. poreCov is freely available on GitHub under the GNUv3 license: github.com/replikation/poreCov.
ISSN:1664-8021
1664-8021
DOI:10.3389/fgene.2021.711437