QIIME vs Mothur vs UPARSE

[dannybiofilm]

Hello,

I am working on a pipeline to analyze some metabarcoding DNA samples from a MiSeq. I have read multiple papers that all use different programs for OTU clustering. Does anyone have suggestions on programs that work best (QIIME, Mothur, or UPARSE).

Thanks

[thermophile]

what kind of metabarcode target? Can your target be aligned? If so, mothur. If not, doesn't matter as much. I like mothur because of many reasons including it's easy to install natively (my datasets are too big to mess with qiime's virtualbox workaround)

[dannybiofilm]

Thanks for responding, I am targeting 16S, 18S, and 23S with 3 different primer sets. However, I will be analyzing each of them separately.

[thermophile]

Use mothur with the silva alignment. you may need to format the LSU alignment for mothur but there are instructions on the mothur website. Also the mothur forum is fairly active if you have any issues.