FORUMBest/easiest analysis pipeline for 16s sequencing?
Franzi Graef asked 4 months ago

  • Hi,
    what is a good software or pipeline to analyze 16s MiSeq data for human microbiota samples for someone who does not have a bioinformatics background?

    4 Answers
    rcorbett Staff answered 4 months ago

  • Hi Franzi,
    If you can get it running (it likely requires some knowledge of working with the command line and illumina data), people here have had good success with running Mothur on MiSeq data:

    flefebvre Staff answered 4 months ago

  • You can also try the Bioconductor package dada2. In additional to having all processing steps implemented and being parallelized,  It infers exact sequence variants which in many people’s opinion is the superior paradigm. It is also dead easy to use from the R command line and connects well to downstream packages such as phyloseq. Microbiomeanalyst ( is also nice to use for simple downstream analyses.

    jrosner Staff answered 4 months ago

  • You can also have a look at this research article that compares 3 tools — mothur, QIIME, and MG-RAST.

    Phillip A Richmond answered 4 months ago

  • I’ve used QIIME, developed by a lab that I used to collaborate with at the University of Colorado under Rob Knight (now at UCSD). QIIME is well suited for numerous metagenomic analyses, and the tutorials are straightforward and wrapped into jupyter-notebooks, which makes learning the pipeline very accessible.