Abundance Calculation in MetaPhlAn 3: Methodology, TPM or RPKM, and the Treatment of Unclassified Reads

Question

[ramin.k2013]

In MetaPhlAn 3, how is abundance calculated, given that it factors in gene length and total sequence count? Is this achieved through TPM (Transcripts Per Million) or RPKM (Reads Per Kilobase Million)? Furthermore, are unclassified reads omitted from the abundance estimation process in MetaPhlAn 3?

[Ram]

Please do not use bioinformatics as a tag unless your post is about the field of bioinformatics itself. I've cleaned up the tags in your posts this time.

[ramin.k2013]

Actually, MetaPhlan3 is one of the bioinformatics pipelines used for microbial analysis and I do not get why "bioinformatics" tag can't be relatable. Sorry for the confusion.