Metagenomes assembly is arguably more difficult than genome assembly, because metagenomes have characteristics of genomes (repeats) as well as transcriptomes (different subgenomes present at different levels). Titus Brown’s group posted an interesting paper at arxiv.org few weeks back, and we hope you will enjoy it. We started reading it but got scared within first paragraph, when they mentioned future goal of assembling a 20 Tb library !!
Adina Chuang Howe, Janet Jansson, Stephanie A. Malfatti, Susannah G. Tringe, James M. Tiedje, C. Titus Brown
The large volumes of sequencing data required to sample complex environments deeply pose new challenges to sequence analysis approaches. De novo metagenomic assembly effectively reduces the total amount of data to be analyzed but requires significant computational resources. We apply two pre-assembly filtering approaches, digital normalization and partitioning, to make large metagenome assemblies more comput\ ationaly tractable. Using a human gut mock community dataset, we demonstrate that these methods result in assemblies nearly identical to assemblies from unprocessed data. We then assemble two large soil metagenomes from matched Iowa corn and native prairie soils. The predicted functional content and phylogenetic origin of the assembled contigs indicate significant taxonomic differences despite similar function. The assembly strategies presented are generic and can be extended to any metagenome; full source code is freely available under a BSD license.
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On the topic of scalable metagenome assembler, readers may also like to read about Ray Meta covered here. C. Titus Brown, author of paper linked above, was also a reviewer of Ray Meta paper. His review opinions are posted here in his blog.
You used “I”! Seriously, you have a good blog but the “we” thing is weird. I can’t recall any of the other bloggers that do it when just referring to themselves. To be brutally honest it kind of makes you come abroad as pretentious. It is a blog, you are allowed to be personal without diluting your point. Go on, you know you want to.
The blog has two primary purposes – (i) to present high-quality discussion of scientific topics and write on them as objectively and impersonally as possible, (ii) to point out various hypocrisies of top journals, US academia and their backers in government. The stylistic choices we made are consistent with those goals.
We *do not* want to draw attention to the narrator to present our views, and get comments like ‘he is an Israeli and all Israelis are crooks’, or ‘he is a left-wing nut and all left-wing nuts are against military’ or ‘he is a right-wing nut, who does not believe in evolution’. You may say that such views are not common among scientists, but we have shown you an example yesterday disproving that point. Why should PLOS journal want to increase ‘diversity’ among its academic editors, if it does not believe that their academic editors are racist, sexist or biased in favor whatever group they identify with?
In the big picture, this blog is an experiment with social media and we made certain choices for the experiment. Maybe the choices we made are wrong and the ‘experiment’ will fail, or maybe the choices are right. We shall find out soon. One thing for sure, we do seek your attention and that is why we write. However, we like to attract your attention only through the quality of our contents and in no other way. Also, we feel honored that you chose to express your views here and we take all criticisms positively.
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