tetano
Editor, Senior Moderator
BMC Genomics
. 2024 Jun 28;25(1):647.
doi: 10.1186/s12864-024-10539-0. UnCoVar: a reproducible and scalable workflow for transparent and robust virus variant calling and lineage assignment using SARS-CoV-2 as an example
Alexander Thomas[SUP] #[/SUP][SUP] 1 [/SUP], Thomas Battenfeld[SUP] #[/SUP][SUP] 1 [/SUP], Ivana Kraiselburd[SUP] 1 [/SUP], Olympia Anastasiou[SUP] 2 [/SUP], Ulf Dittmer[SUP] 2 [/SUP], Ann-Kathrin Dörr[SUP] 1 [/SUP], Adrian Dörr[SUP] 1 [/SUP], Carina Elsner[SUP] 2 [/SUP], Jule Gosch[SUP] 1 [/SUP], Vu Thuy Khanh Le-Trilling[SUP] 2 3 [/SUP], Simon Magin[SUP] 1 [/SUP], René Scholtysik[SUP] 3 [/SUP], Pelin Yilmaz[SUP] 1 [/SUP], Mirko Trilling[SUP] 2 3 [/SUP], Lara Schöler[SUP] 2 3 4 [/SUP], Johannes Köster[SUP] #[/SUP][SUP] 5 6 [/SUP], Folker Meyer[SUP] #[/SUP][SUP] 7 [/SUP]
Affiliations
Background: At a global scale, the SARS-CoV-2 virus did not remain in its initial genotype for a long period of time, with the first global reports of variants of concern (VOCs) in late 2020. Subsequently, genome sequencing has become an indispensable tool for characterizing the ongoing pandemic, particularly for typing SARS-CoV-2 samples obtained from patients or environmental surveillance. For such SARS-CoV-2 typing, various in vitro and in silico workflows exist, yet to date, no systematic cross-platform validation has been reported.
Results: In this work, we present the first comprehensive cross-platform evaluation and validation of in silico SARS-CoV-2 typing workflows. The evaluation relies on a dataset of 54 patient-derived samples sequenced with several different in vitro approaches on all relevant state-of-the-art sequencing platforms. Moreover, we present UnCoVar, a robust, production-grade reproducible SARS-CoV-2 typing workflow that outperforms all other tested approaches in terms of precision and recall.
Conclusions: In many ways, the SARS-CoV-2 pandemic has accelerated the development of techniques and analytical approaches. We believe that this can serve as a blueprint for dealing with future pandemics. Accordingly, UnCoVar is easily generalizable towards other viral pathogens and future pandemics. The fully automated workflow assembles virus genomes from patient samples, identifies existing lineages, and provides high-resolution insights into individual mutations. UnCoVar includes extensive quality control and automatically generates interactive visual reports. UnCoVar is implemented as a Snakemake workflow. The open-source code is available under a BSD 2-clause license at github.com/IKIM-Essen/uncovar.
Keywords: Lineage assignment; Next generation sequencing; SARS-CoV-2; Variant calling; Workflow.
. 2024 Jun 28;25(1):647.
doi: 10.1186/s12864-024-10539-0. UnCoVar: a reproducible and scalable workflow for transparent and robust virus variant calling and lineage assignment using SARS-CoV-2 as an example
Alexander Thomas[SUP] #[/SUP][SUP] 1 [/SUP], Thomas Battenfeld[SUP] #[/SUP][SUP] 1 [/SUP], Ivana Kraiselburd[SUP] 1 [/SUP], Olympia Anastasiou[SUP] 2 [/SUP], Ulf Dittmer[SUP] 2 [/SUP], Ann-Kathrin Dörr[SUP] 1 [/SUP], Adrian Dörr[SUP] 1 [/SUP], Carina Elsner[SUP] 2 [/SUP], Jule Gosch[SUP] 1 [/SUP], Vu Thuy Khanh Le-Trilling[SUP] 2 3 [/SUP], Simon Magin[SUP] 1 [/SUP], René Scholtysik[SUP] 3 [/SUP], Pelin Yilmaz[SUP] 1 [/SUP], Mirko Trilling[SUP] 2 3 [/SUP], Lara Schöler[SUP] 2 3 4 [/SUP], Johannes Köster[SUP] #[/SUP][SUP] 5 6 [/SUP], Folker Meyer[SUP] #[/SUP][SUP] 7 [/SUP]
Affiliations
- PMID: 38943066
- PMCID: PMC11214259
- DOI: 10.1186/s12864-024-10539-0
Background: At a global scale, the SARS-CoV-2 virus did not remain in its initial genotype for a long period of time, with the first global reports of variants of concern (VOCs) in late 2020. Subsequently, genome sequencing has become an indispensable tool for characterizing the ongoing pandemic, particularly for typing SARS-CoV-2 samples obtained from patients or environmental surveillance. For such SARS-CoV-2 typing, various in vitro and in silico workflows exist, yet to date, no systematic cross-platform validation has been reported.
Results: In this work, we present the first comprehensive cross-platform evaluation and validation of in silico SARS-CoV-2 typing workflows. The evaluation relies on a dataset of 54 patient-derived samples sequenced with several different in vitro approaches on all relevant state-of-the-art sequencing platforms. Moreover, we present UnCoVar, a robust, production-grade reproducible SARS-CoV-2 typing workflow that outperforms all other tested approaches in terms of precision and recall.
Conclusions: In many ways, the SARS-CoV-2 pandemic has accelerated the development of techniques and analytical approaches. We believe that this can serve as a blueprint for dealing with future pandemics. Accordingly, UnCoVar is easily generalizable towards other viral pathogens and future pandemics. The fully automated workflow assembles virus genomes from patient samples, identifies existing lineages, and provides high-resolution insights into individual mutations. UnCoVar includes extensive quality control and automatically generates interactive visual reports. UnCoVar is implemented as a Snakemake workflow. The open-source code is available under a BSD 2-clause license at github.com/IKIM-Essen/uncovar.
Keywords: Lineage assignment; Next generation sequencing; SARS-CoV-2; Variant calling; Workflow.