Notes for dealing with metabarcoding sequence data.


Siobhon Egan


July 30, 2021


Analysis of amplicon metabarcoding next generation sequencing data

🔗 Useful resources

Additional analysis


Sample size calculator

Links to some useful resources for calculating power and sample size in microbiome studies. Good for grant and project proposals to show you have thought about sample size etc.

Some general points to consider

  • What population should I target?
  • How should I collect and store the samples? (CONTROLS!!!)
  • What am I targeting and how should i extract?
  • What sequencing approach should I use, amplicon or whole shotgun metagenome? Will there be PCR involved or do I want a pre-PCR library preparation method?
  • How deeply should I sequence?


  • Mattiello F, Verbist B, Faust K, Raes J, Shannon WD, Bijnens L, Thas O. A web application for sample size and power calculation in case-control microbiome studies. Bioinformatics. 2016 Jul 1;32(13):2038-40. doi: 10.1093/bioinformatics/btw099
  • Kelly BJ, Gross R, Bittinger K, Sherrill-Mix S, Lewis JD, Collman RG, Bushman FD, Li H. Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA. Bioinformatics. 2015 Aug 1;31(15):2461-8. doi: 10.1093/bioinformatics/btv183
  • Casals-Pascual C, González A, Vázquez-Baeza Y, Song SJ, Jiang L, Knight R. Microbial Diversity in Clinical Microbiome Studies: Sample Size and Statistical Power Considerations. Gastroenterology. 2020 May;158(6):1524-1528. doi: 10.1053/j.gastro.2019.11.305.