Hi, We performed shotgun metagenomics for dozens of stool samples. Next, we assembled the reads into contigs and binned the contigs to reconstruct the genomes. We want to use the reconstructed metagenomes in order to calculate the abundance of the microbes they represent in all samples.
- Is there any recommended aligner (and parameters) for such task? (considering that we align against not-full genomes, multimapping etc.)
- I came across some studies that calculated relative abundance by dividing the number of reads aligned to a metagenome by the total number of reads of a sample. Any Idea why genome length was not also taken into account?
- Is there any reason to calculate absolute abundance in such case? (maybe for downstream analyses/tools?)