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Do I have enough reads for virome analyis?

Hi,

I have performed Illumina Hiseq metagenomic sequencing in ~200 samples of the upper respiratory system of patients and healthy volunteers. After removing human DNA, my samples contain ~2 Million microbial reads - the vast majority of them bacterial.

Nonetheless I would like to check if I can perform an analysis only in my viral reads. The problem is that when I am looking only at viral reads as these were assigned by Kaiju I have on average ~700 viral reads, with some samples containing even less than 100 reads. As expected, my rarefaction curves don't reach a plateau and whatever signal I have in my alpha and beta diversity plots from my bacterial reads is completely lost when I am looking at the virome of the two groups.

Based on that information can I claim that the viral reads of my dataset are very poor and should not be interrogated further? Is there another way to asses if the number of viral reads I have are enough for statistical analysis?

Thank you in advance for your help. Leonardos

metagenomics hiseq virome statistics reads
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updated by Bruntland Aldre • Bruntland Aldre • written by Mageiros • Mageiros

Hi there Leonardos,

May I ask did you reach plateau with your entire 2 million microbial reads?

From my reading, I suppose you can consider a metagenome is "deep" if you reach 20-30 million reads. 2 million reads may be a bit underrepresented. I may be wrong.

As for the case of viral reads, they are usually of very low relative abundance when you do bulk sequencing. You might get higher relative abundance if you concentrate the viral particles and/or filter them prior to DNA extraction. From my understanding. I hope it helps.

Cheers, ~ Aldre

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written by Bruntland Aldre • Bruntland Aldre

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