The most obvious (and probably the most used) source of reference sequences (or any kind of sequences) is the NCBI Nucleotide database and its “sister” sites: the EBI European Nucleotide Archive, and the DNA Data Bank of Japan.
All three sites provide some kind of search functionality and a few (shorter) sequences can be downloaded from the result pages directly, in multiple formats. For larger reference sequences (e.g. full human or mouse chromosomes or full genomes) or a long list of references the ftp sites or batch query tools should be used.
Ftp sites:
Batch search/Download tools:
There are some other pages with a more limited focus, that can be very useful for retrieving reference sequences:
Tip: the Genome Analysis Toolkit (GATK) needs the human chromosomes in a special order (karyotypic, to be precise). Different versions of the karyotypically sorted human genome are provided by the GATK team as a resource bundle, which can be downloaded from their ftp site.
