As someone who uses the MiSeq platform for high-throughput DNA amplicon sequencing, I was excited to see a new paper in Applied & Environmental Microbiology that presents a pipeline for processing these data. Users of the program "mothur" were sent an email announcing the publication:
"Hello mothur users...
I know many of you have been interested in our protocols and the ideas behind our new MiSeq SOP. We have some great news - the manuscript that we've been working on has been accepted to Applied and Environmental Microbiology. As of today, it is available online ahead of publication. You can find the manuscript here:
Until it's published, if you would like the supplement please let me know and I'll send it your way.
So mothur now may become the program of choice for those studying microbial diversity using the MiSeq. Currently, I am using a hybrid approach, with PANDAseq for read assembly, mothur for screening, and QIIME for everything else. However, it is difficult to argue with the notion that it's always easier to use a single program!