Metagenomic Mappers & Benchmark Datasets?

Question

[jnowacki]

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?

Answer 1

[Samuel Brady]

Taxonomer gives very rapid, visual, interactive output using an online format. It can rapidly determine the microbial composition of your sample using a sampling of your fastq read inputs.

The paper is here.