VEO MPXV Taskforce Analysis

All public MPXV INSDC raw read data is systematically analysed to produce a set of uniform variant calls (VCF format) and consensus sequences, using the COVID Sequence Analysis Workflow and the Nanopore Analysis Workflow. Briefly, reads are mapped to the MPXV reference genome, variants are called using LoFreq and annotated using SnpEff. Variant sets are filtered and used to construct consensus sequences. 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. This work is carried out as part of the Versatile emerging infectious disease observatory (VEO) project, a collaboration between: EMBL-EBI Erasmus Medical Center (EMC), Netherlands Eötvös Loránd University (ELTE), Hungary Technical University of Denmark, Denmark