Trying to download the cow genome (again): where's the beef (again)?

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.

Community annotation — by any name — still isn’t a part of the research process. It should be →

In order for community annotation efforts to succeed, they need to become part of the established research process: mine annotations, generate hypotheses, do experiments, write manuscripts, submit annotations. Rinse and repeat.

A thoughtful post by Todd Harris on his blog which lists some suggestions for how to fix the failure of community annotation projects.

I particularly like Todd's 3rd suggestion:

We need to recognize the efforts of people who do [community annotation]. This system must have professional currency to it, akin to writing a review paper, and should be citable…

Tales of drafty genomes: part 3 – all genomes are complete…except for those that aren't

This is the third post in an infrequent series that looks at the world of unfinished genomes.

One of the many, many resources at the NCBI is their Genome database. Here's how they describe themselves:

The Genome database contains sequence and map data from the whole genomes of over 1000 species or strains. The genomes represent both completely sequenced genomes and those with sequencing in-progress. All three main domains of life (bacteria, archaea, and eukaryota) are represented, as well as many viruses, phages, viroids, plasmids, and organelles.

This text could probably be updated because the size of the database is now wrong by an order of magnitude…there are currently 11,322 genomes represented in this database. But how many of them are 'completely sequenced' and how many are at the 'sequencing in-progress' stage?

Luckily, the NCBI classifies all genomes into one of four 'levels':

• Complete
• Chromosome
• Scaffold
• Contig

I couldn't find any definitions for these categories within the NCBI Genome database, but elsewhere on the NCBI website I found the following definitions for the latter three categories:

Chromosome - there is sequence for one or more chromosomes. This could be a completely sequenced chromosome (gapless) or a chromosome containing scaffolds with unlinked gaps between them.

Scaffold - some sequence contigs have been connected across gaps to create scaffolds, but the scaffolds are all unplaced or unlocalized.

Contig - nothing is assembled beyond the level of sequence contigs

So considering just the 2,032 Eukaryotic species in the NCBI Genome Database, we can ask…how many of them are complete?

Completion status of 2,032 eukaryotic genomes, as classified by NCBI

The somewhat depressing answer is that only a meagre 24 eukaryotic genomes are listed as complete, about 1% of the total. Even if we include genomes with chromosome sequences, we are still only talking about 13% of all genomes. You might imagine that the state of completion would be markedly better when looking at prokaryotes. However, only 11.5% of the 31,696 prokaryotic genomes are classified as complete.

In the last post in this series, I included a dictionary definition of the word 'draft'. This time, let's look to see how Merriam-Webster defines 'complete':

having all necessary parts : not lacking anything

not limited in any way

not requiring more work : entirely done or completed

By this definition, I think we could all agree that very few genomes are actually complete.

Choosing names for bioinformatics software: it's a snap

Image from flickr user plashingvole

Compare the following published bioinformatics resources:

1. SNAP: Semi-HMM-based Nucleic Acid Parser (published 2004)
2. SNAP: Suite of Nucleotide Analysis Programs (published 2005)
3. SNAP: SNP Annotation And Proxy search (published 2008)
4. SNAP: Screening for NonAcceptable Polymorphisms (published 2008)
5. SNAP: Scalable Nucleotide Alignment Program (published 2011)

Every new bioinformatics tool that decides to reuse an existing name — either wilfully or by ignorance — makes it that little bit harder for people to find one of the other similarly-named-tools that they might be searching for.

h/t to @byuhobbes for bringing some of these duplicates to my attention.