ena-STUDY-EMBL-EBI-07-06-2021-16:19:31:108-735
Filtered variant calls of public SARS-CoV-2 reads
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 VCF files that have been filtered using an allele frequency (AF) threshold of 0.25. VCFs produced within this project are also streamed into the European Variation Archive (EVA) and accessioned as Sequence Variation Objects. <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 VCF files that have been filtered using an allele frequency (AF) threshold of 0.25. VCFs produced within this project are also streamed into the European Variation Archive (EVA) and accessioned as Sequence Variation Objects. <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>