Is Mothur the only metagenomic toolset that provides the number of sequences/OTU? I would love to use map with BWA-MEM/Bowtie2 and get abundances but I don’t see how
There is probably a way to do it with BWA but this is not common practice. In the basics you use a cluster algorithm from packages like USEARCH, VSEARCH, DADA2 etc. (I dont know what is avaible on public galaxy servers) And after clustering you can create something what is called a OTU table. A OTU table can be created with other tools/scripts that are also part of the above mentioned packages.
So the answer to your question is no, Mothur is not the only package that can do this. Just saw that DADA2 is available on public galaxy.
I am also not sure if you are sure and asking the right question. Most of the time if you talk about OTU’s you don’t talk about metagenomics. OTU’s focuses mostly on targeted barcodes/amplicons and not full genomes.
you can use MetaPhlAn2 to profile the composition of microbial communities. It allows providing the SAM file generated by Bowtie2 as input.
In addition to @gallardoalba answer an alternative to MetaPhlan2 can be kraken. I don’t know if that tool is good but it is on galaxy.