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Old 04-11-2014, 05:11 PM   #1
AndrewRGross
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Default Using Whole Genome Amplification (WGA) during metagenome prep

My lab is going to prepare a metagenome soon and my PI is inclined to use Multiple Displacement Amplification (MDA) for Whole Genome Amplification (WGA). The samples are from rocks from within the ocean crust with attached biofilms. Biomass is very low and diversity is typically moderate to high. I've heard from several people that MDA produces such large biases in the sequenced library that it hinders assembly and inspires concern in reviewers when trying to publish results.

Is this true, or am I being too paranoid? If I'm right, can anyone offer a strong explanation or peer-reviewed source to present to the PI?

Thanks
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Old 04-16-2014, 07:48 AM   #2
cliffbeall
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I found these two papers that show that there probably would be biases. However, SPAdes or khmer dignorm might be able to help with the assembly.

Could you do 16S profiling to get (semi-)quantitative compositional info?

Multiple displacement amplification compromises quantitative analysis of metagenomes
Amplification Methods Bias Metagenomic Libraries of Uncultured Single-Stranded and Double-Stranded DNA Viruses
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