Hello, I am new to NGS analysis and am considering using MeFit to merge and filter my 16s rRNA data from MiSeq. I requested PE300 (now I regret it) for V3-4 and the reverse read is poor. This program will allow me to keep the sequences that don't actually overlap in the analysis. It sounds really great and will let me use mothur to complete the analysis, I am currently using mothur from step one. I just don't know if MeFit it is really going to work to improve my data and I don't understand enough to really assess this based on what the paper says so I'm asking for help to figure this out. Here is a link to the paper: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1358-1
Any input from people who have done this before (analysis with NGS or using MeFit) would be greatly appreciated!