Do I have enough reads for virome analyis?
Entering edit mode
7 weeks ago
Mageiros • 0


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 • 134 views

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