Celera Genomics used whole genome shotgun sequencing to sequence the mouse genome

The Mus musculus genome was sequenced and annotated by Celera Genomics to study the evolution of different mammalian species. The combined whole genome shotgun assembly was deposited in Genbank under the WGS project accession AAHY00000000. This assembly contains 27 million Celera reads on four Mus musculus strains (129X1/SvJ, 129S1/SvImJ, DBA/2J and A/J), 13 million reads on C57BL/6 from the NCBI Trace Archive, 0.4 million BAC end sequences from TIGR, and unfinished and finished BACs pulled from NCBI. The assembly process relied on Celera's paired reads and BAC end reads for long range order and orientation. Its scaffolds were mapped to chromosomes using STS maps.