Reference quality genomes
By the end of 2022, we expect to have high quality reference genomes and annotation available for seventeen inbred mouse strains. Extensive work has gone into producing the first set of truly reference quality genomes (comparable to GRCm39). Links to these genomes will be posted here when they are available.
Draft (short read) genomes
In 2018, we produced the first draft reference genomes for sixteen inbred strains (described in this paper). Whilst these genomes were informative for establishing the extent of non-reference haplotype variation and have very good representation for protein coding genes, we do not recommend using them for NGS analysis due to the lack of representation for common repeat sequences. These genomes can be found from Ensembl.