How to do alpha and beta diversity with shougun metagenome data

Question

[jeccy.J]

Hi Everyone,

Can anyone suggest me any tools or R package for shotgun metagenome alpha and beta diversity analysis. Currently i am using kaiju for classification of all the raw reads. I have a final csv file with the taxa abundance (number of total reads) of each sample. For example :

      sample1    sample2  sample3 

taxa1:  30            40            50   
taxa2 :  50            60            100

Now i would like to run any statistical analysis which will provide me which taxa is have a significant difference across the samples?

Answer 1

[gb]

https://www.drive5.com/usearch/manual/cmd_alpha_div.html

https://www.drive5.com/usearch/manual/cmd_beta_div.html

[lagartija]

I think this is ment for barcoding data. Are you saying we can adapt the method ? Is is certainly possible to change OTU by taxonomic assignment but is it statistacally correct ?