The genome of a red fox (Vulpes vulpes) was recently sequenced and assembled usingnext-generation sequencing (NGS). The assembly is of high quality, with 94X coverage and ascaffold N50 of 11.8 Mbp, but is split into 676,878 scaffolds, some of which are likely to containassembly errors. Fragmentation and misassembly hinder accurate gene prediction and downstreamanalysis such as the identification of loci under selection. Therefore, assembly of the genome intochromosome-scale fragments was an important step towards developing this genomic model.Scaffolds from the assembly were aligned to the dog reference genome and compared to thealignment of an outgroup genome (cat) against the dog to identify syntenic sequences among species.The program Reference-Assisted Chromosome Assembly (RACA) then integrated the comparativealignment with the mapping of the raw sequencing reads generated during assembly against thefox scaffolds. The 128 sequence fragments RACA assembled were compared to the fox meioticlinkage map to guide the construction of 40 chromosomal fragments. This computational approach toassembly was facilitated by prior research in comparative mammalian genomics, and the continuedimprovement of the red fox genome can in turn offer insight into canid and carnivore chromosomeevolution. This assembly is also necessary for advancing genetic research in foxes and other canids.