Consensus genomes
These consensus genomes represent those generated from a mumps outbreak in Washington in 2016, in addition to a sampling of mumps genomes collected from all over the US from 2006 to present. These genomes were used in a paper describing the mumps outbreak, and have also been deposited in public databases for others to use. Consensus genomes are freely available in Genbank under accession numbers MT859507-MT859672, and raw fastq files with all human reads removed are available on the Short Read Archive under BioProject PRJNA641715. A key that links the strain names as shown in this repository to the bioproject accessions is available here.
During the process of doing this project, we renamed strains a few times. All sequences currently here contain the strain names as used and displayed on nextstrain.org/mumps and as deposited in Genbank. However, if you accessed and used these genomes previously, we have included a name key to convert between these new strain names and the ones listed previously.