Protocols for sequencing mumps viruses

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 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.