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9.2 years ago
bioinfo
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Hi
I have noticed many people struggle to assemble even just only one metagenome dataset. Recently I have been thinking to assemble many metagenomes (>100) in a quick and easy way (in parallel?) within a few days using a common criteria/default settings for all. I don't have to be too strict in assembly but just want to run in default settings on any of the available assembler(s) to get thousands/millions of contigs. Any suggestions?
This is the first I heard of the portal. It says there "the EBI Metagenomics team will access them and perform the analysis" but it is not clear there what that means. A link on another page mentions 16S rRNA analysis via QIIME. Do you also offer metagenome assembly as well (as the OP needs)?
It's pretty new. I'm not completely familiar with it, to be honest; I saw Rob Finn (in charge of the project) give a talk on it a couple of weeks ago and thought it might be useful. His talk is here if you'd like to take a look. From what I remember/can piece together from a brief glance at the presentation, they don't actually do assemblies as it's too error-prone and actually doesn't improve the analysis. Instead they assemble genes and analyse for GO terms and protein domains to determine the activity of the metagenome.