adbc7095-05a2-48a9-a198-6ab3eb3abadb
Consensus sequences produced by VEO SARS-CoV-2 Taskforce
All public SARS-CoV-2 INSDC raw read data is systematically analysed to produce a set of uniform variant calls (VCF format) and consensus sequences, using the <a href="https://github.com/enasequence/covid-sequence-analysis-workflow">COVID Sequence Analysis Workflow</a> and the <a href="https://github.com/dnieuw/ENA_SARS_Cov2_nanopore">Nanopore Analysis Workflow</a>. Briefly, reads are mapped to the SARS-CoV-2 reference genome, variants are called using <a href="https://csb5.github.io/lofreq/">LoFreq</a> and annotated using <a href="http://pcingola.github.io/SnpEff/">SnpEff</a>. Variant sets are filtered and used to construct consensus sequences. <br></br> This project holds consensus sequences, which have been constructed from filtered variant calls as per <a href="https://www.ebi.ac.uk/ena/browser/view/PRJEB45554">PRJEB45554</a>. Ambiguous base calls in the consensus are marked with Ns. <br></br> This work is carried out as part of the <a href="https://www.veo-europe.eu/">Versatile emerging infectious disease observatory (VEO) project</a>, a collaboration between: <ul>     <li><a href="https://www.ebi.ac.uk/">EMBL-EBI</a></li>     <li><a href="https://www.erasmusmc.nl/en">Erasmus Medical Center (EMC), Netherlands</a></li>     <li><a href="https://www.elte.hu/en/">Eötvös Loránd University (ELTE), Hungary</a></li>    <li><a href="https://www.dtu.dk/english">Technical University of Denmark, Denmark</a></li> </ul>
All public SARS-CoV-2 INSDC raw read data is systematically analysed to produce a set of uniform variant calls (VCF format) and consensus sequences, using the <a href="https://github.com/enasequence/covid-sequence-analysis-workflow">COVID Sequence Analysis Workflow</a> and the <a href="https://github.com/dnieuw/ENA_SARS_Cov2_nanopore">Nanopore Analysis Workflow</a>. Briefly, reads are mapped to the SARS-CoV-2 reference genome, variants are called using <a href="https://csb5.github.io/lofreq/">LoFreq</a> and annotated using <a href="http://pcingola.github.io/SnpEff/">SnpEff</a>. Variant sets are filtered and used to construct consensus sequences. <br></br> This project holds consensus sequences, which have been constructed from filtered variant calls as per <a href="https://www.ebi.ac.uk/ena/browser/view/PRJEB45554">PRJEB45554</a>. Ambiguous base calls in the consensus are marked with Ns. <br></br> This work is carried out as part of the <a href="https://www.veo-europe.eu/">Versatile emerging infectious disease observatory (VEO) project</a>, a collaboration between: <ul>     <li><a href="https://www.ebi.ac.uk/">EMBL-EBI</a></li>     <li><a href="https://www.erasmusmc.nl/en">Erasmus Medical Center (EMC), Netherlands</a></li>     <li><a href="https://www.elte.hu/en/">Eötvös Loránd University (ELTE), Hungary</a></li>    <li><a href="https://www.dtu.dk/english">Technical University of Denmark, Denmark</a></li> </ul>