16s rrna data analysis

Can I use MEGAN6 to analyze 16s rrna metagenomic data? (taxonomic/OTU analysis)

If not, could you recommend few softwares for such analysis? Thank you.

Yes, you definitely can analyse your 16S rRNA data. There are multiple options to do that.
One option is that you analyse them with your tool of choice (for example QIIME) and import the resulting BIOME files into MEGAN to further analyse the data.
The other option is to do an alignment based analysis of your raw reads. This means you will have to preprocess your reads (demultiplex, trim and clip as you want it) and then select a database to align to (I recommend SILVA or the NCBI 16S microbial.)
For this database get the original fasta sequences it was built on and use them to generate a MALT index. Now you can align your reads to that MALT index which will generate an RMA file that you can directly open with MEGAN. This is a taxonomic analysis, but not based on OTUs. Theoretically you could also use any clustering tool to find OTUs, select representative sequences and align only those sequences. In my own opinion, I get more realistic results aligning all preprocessed reads and skipping the clustering step.
I will try and write a more detailed tutorial on how to do this and put it in our tutorial section as soon as possible.