I am trying to compare metagenomics datasets without biological replicates. (Not ideal, i know. But biological replication is not possible for the communities we want to learn about.) Right now I'm working with normalized count data, but I've got raw reads and am happy to recompute anything.
I would like to rank features by how much their abundance decreases or increases between samples. Basically i want log2 fold changes. But those get too unreliable when read counts for a feature are low/zero. GFOLD looks like what i need, but the tool is not available anymore.
Do you have any recommendations regarding either a specific tool or relevant texts? I'm not set on using fold changes, open to basically anything that helps with comparing the datasets.
*edit: Thanks to the corresponding authors i found GFOLD at a new URL.