I am only starting now to investigate the microbiome during my master’s degree and I was wondering if alpha-diversity indices would still be relevant after filtering since they are calculated from estimated unobserved species (that are based on species that are observed only once, or twice with jacknife 2…).
My team is using c=0,005% as recommended by Bokulich in 2013 but while getting rid of sequencing errors and polymerisation errors I am afraid we also lose useful information.
Thanks a lot for your answers,
Master’s Degree in Animal Nutrition
Vet School Student in Toulouse, France.