min_otu_size in pick_otus.py ?

[ElianneEgge]

Hi!
I am using pick_otus.py with method swarm to pick otus. I was wondering if there is a way to remove low-abundant otus when I use this method? I looked through the parameter options (pick_otus.py -h) but there does not seem to be an option similar to min_otu_size (as in pick_open_reference_otus.py). I realise I can remove low-abundant otus from the otu table I obtain in the end with filter_otus.., however I thought it would be more efficient to remove them prior to chimera check (?). Or is it better to keep them in the dataset during chimera detection?

Best regards,
Elianne Egge,
Post.-Doc.
Dept. of Biosciences
Univeristy of Oslo

[Colin Brislawn]

Hello Elianne,

It probably would be more efficient to remove OTUs prior to chimera checking, but I'm not sure the best way to do this with swarm.

Take a look at the pipeline described by Frédéric Mahé, in which he described this process. 

https://github.com/frederic-mahe/swarm/wiki/Fred's-metabarcoding-pipeline#global-dereplication-clustering-and-chimera-detection 

Notice, he does chimera checking before OTU picking. At this step, you could also remove low abundance sequences. Then you take these reads and pass them into OTU picking with Swarm. 

I know that does not directly answer your question, but I hope the notes of the swarm developer helps. He would be a great point of contact here too. 

Colin 

[ElianneEgge]

Thanks for your quick reply. I'll check out the link and ask the swarm developers.

Best,
Elianne