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2021-07-28Zeitschriftenartikel
poreCov-An Easy to Use, Fast, and Robust Workflow for SARS-CoV-2 Genome Reconstruction via Nanopore Sequencing
dc.contributor.authorBrandt, Christian
dc.contributor.authorKrautwurst, Sebastian
dc.contributor.authorSpott, Riccardo
dc.contributor.authorLohde, Mara
dc.contributor.authorJundzill, Mateusz
dc.contributor.authorMarquet, Mike
dc.contributor.authorHölzer, Martin
dc.date.accessioned2024-06-05T13:46:16Z
dc.date.available2024-06-05T13:46:16Z
dc.date.issued2021-07-28none
dc.identifier.other10.3389/fgene.2021.711437
dc.identifier.urihttp://edoc.rki.de/176904/11683
dc.description.abstractIn 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 via 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.eng
dc.language.isoengnone
dc.publisherRobert Koch-Institut
dc.rights(CC BY 3.0 DE) Namensnennung 3.0 Deutschlandger
dc.rights.urihttp://creativecommons.org/licenses/by/3.0/de/
dc.subjectNextfloweng
dc.subjectbioinformaticseng
dc.subjectcoronavirus - COVID-19eng
dc.subjectlineageseng
dc.subjectdockereng
dc.subjectSARS-CoV-2eng
dc.subjectpipelineeng
dc.subjectnanopore sequencingeng
dc.subject.ddc610 Medizin und Gesundheitnone
dc.titleporeCov-An Easy to Use, Fast, and Robust Workflow for SARS-CoV-2 Genome Reconstruction via Nanopore Sequencingnone
dc.typearticle
dc.identifier.urnurn:nbn:de:0257-176904/11683-7
dc.type.versionpublishedVersionnone
local.edoc.container-titleFrontiers in Geneticsnone
local.edoc.container-issn1664-8021none
local.edoc.pages8none
local.edoc.type-nameZeitschriftenartikel
local.edoc.container-typeperiodical
local.edoc.container-type-nameZeitschrift
local.edoc.container-urlhttps://www.frontiersin.org/journals/geneticsnone
local.edoc.container-publisher-nameFrontiers Meadia S.A.none
local.edoc.container-volume12none
local.edoc.container-reportyear2021none
dc.description.versionPeer Reviewednone

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