Estimation of absolute abundances

[IrSoler]

Dear developers,

I have paired-end sequencing fastqc files from different samples and I would like to perform the phylogenetic abundance table based on the GTDB reference. Your singlem pipe tool has this objective, but as a result we get the relative abundances table and I would like to get an estimation of the absolute abundances.

Is there any possibility to obtain absolute abundances?

Thank you very much in advance,

Irene

[wwood]

Hi,

Apologies for the slow reponse. I don't think this is possible, at least sticking to the usual meaning of "absolute" abundance. SingleM cannot be used to predict how many total cells (or genome copies) there are in a sample.

It can be used to predict the coverage of a lineage, more sequencing of the same sample will yield more coverage though, so this doesn't estimate abundance in an absolute sense.

HTH, ben