I want to use SparCC for correlation analysis on metagenome samples but it requires raw counts as it has a special way of estimating community composition.
I am completely new to this field and have no idea of what programs can give me raw counts.
Could you suggest a program that does that from Illumina WGS?
So far I have considered Metaphla2 the best option.
But is there a way to make Metaphlan2 output species counts instead of relative abundances?
In its help I have found the options concerning count normalization but I'm not sure they will produce the result I need.