Background: I am developing a pipeline for metagenomic studies of human gut microbiote. In particular, I am mapping the reads data originating from shotgun whole genome sequencing onto a gene catalogue (similar to IGC) and counting reads mapped on each feature/gene. Till now I have been using NGLess, which is a rather convenient tool. However, we have some questions about how exactly it counts reads and it might be not the best option for scaling up our pipeline.
I am looking for alternative tools for gene count. A brief search has shown that
featureCount are two frequently used tools. However they mainly appear in RNAseq context, and I am not certain whether they could be used in my case. I would also appreciate comments on the possibility of using