Assembling many metagenomes in a quick and easy way
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9.2 years ago
bioinfo ▴ 830

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?

metagenomics Assembly • 2.2k views
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9.2 years ago
dago ★ 2.8k

What about SPADES?

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9.2 years ago
Emily 23k

Have you looked at the EBI metagenomics portal?

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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)?

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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.

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9.2 years ago
Vivek Todur ▴ 60

Try MOCAT Pipeline, its quite easy and well suits for the purpose.

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