Very very strange. There is an interesting new metagenomics paper that has come out in Science this week. It is titled “Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota” and it is from the Armbrust lab at U. Washington.
One of the main points of this paper is that the lab has developed software that apparently can help assemble the complete genomes of organisms that are present in low abundance in a metagenomic sample. At some point I will comment on the science in the paper, (which seems very interesting) though as the paper in non Open Access I feel uncomfortable doing so since many of the readers of this blog will not be able to read it.
But something else relating to this paper is worth noting and it is disturbing to me. In a Nature News story on the paper by Virginia Gewin there is some detail about the computational method used in the paper:
“He developed a computational method to break the stitched metagenome into chunks that could be separated into different types of organisms. He was then able to assemble the complete genome of Euryarchaeota, even though it was rare within the sample. He plans to release the software over the next six months.”
What? It is imperative that software that is so critical to a publication be released in association with the paper. It is really unacceptable for the authors to say “we developed a novel computational method” and then to say “we will make it available in six months”. I am hoping the authors change their mind on this but I find it disturbing that Science would allow publication of a paper highlighting a new method and then not have the method be available. If the methods and results in a paper are not usable how can one test/reproduce the work?