b1c523bd-5d0b-4126-8ed5-afcd24d7e993
Systematically called variant data 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 unfiltered variant calls (VCF files) and as such may contain false positives calls and homopolymer errors. BAM files are provided as output by the analysis workflow along with a simple coverage information file. Users are advised to use these in association with the VCFs to perform any filtering tasks prior to using these VCFs for downstream analysis presentation or analysis. <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 unfiltered variant calls (VCF files) and as such may contain false positives calls and homopolymer errors. BAM files are provided as output by the analysis workflow along with a simple coverage information file. Users are advised to use these in association with the VCFs to perform any filtering tasks prior to using these VCFs for downstream analysis presentation or analysis. <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>