I'm looking to map a mixture of bacteria to known references and classify their abundance. What are the top tools for this?
Q1) Top tools for meta-genomics mapping Q2) Control data-sets I can use to verify my metagenomic mapping pipeline?
I am familiar with assembly data-sets and tools. For instance, CAMI is great for assembly benchmarks (Ray, MegaHit, MetaSpades,etc) as well as binning (MaxBin, CONCOCT, MetaBat, etc) but I'm wondering if anyone has done a rundown of mappers in a metagenomic setting? Or if it's as simple as put all your references into a file and map it?