Almost a year ago, I blogged about my frustrations regarding the extremely confusing nature of the cow genome and the many genome assemblies that are out there. Much of that frustration was due to websites and FTP sites that had broken links, misleading information, and woefully incomplete documentation.
One year on and I hear a rumor that a new version of the cow genome is available. So I went off in search of 'UMD 3.1.1'. My first stop was bovinegenome.org which is one place where you can find the previous 'UMD 3.1' assembly. But alas, they do not list UMD 3.1.1.
After some Google searching I managed to find this information at the UCSC Genome Bioinformatics news archive:
We are pleased to announce the release of a Genome Browser for the June 2014 assembly of cow, Bos taurus (BostaurusUMD 3.1.1, UCSC version bosTau8). This updated cow assembly was provided by the UMD Center for Bioinformatics and Computational Biology (CBCB). This assembly is an update to the previous UMD 3.1 (bosTau6) assembly. UMD 3.1 contained 138 unlocalized contigs that were found to be contaminants. These have been suppressed in UMD 3.1.1.
This reveals that the update is pretty minor (removal of contaminant contigs which were never part of any chromosome sequence anyway). In any case, the USCC FTP site contains the UMD 3.1.1 assembly so that's great.
But out of curiosity I followed UCSC's link to the UMD Center for Bioinformatics and Computational Biology (CBCB) website. The home page doesn't make it easy to find the cow genome data. Searching the site for 'UMD 3.1.1' didn't help but searching for 'cow genome' did take me to their Assembly data page which lists the cow genome. Unfortunately the link for the Bos taurus genome takes you to 'page not found'. In contrast, the 'data download' link does work and takes you to their FTP site which fails to include the new assembly (but it does list all of the older cow genome assemblies).
Plus ça change, plus c'est la même chose.