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a-h-b / dadasnake

Amplicon sequencing workflow heavily using DADA2 and implemented in snakemake
GNU General Public License v3.0
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ITSxpress support #36

Open eperezv opened 1 year ago

eperezv commented 1 year ago

Hello,

I like dadasnake and I am using it for processing 16S rRNA amplicons. I have some data from ITS and saw there is support for ITSx. However, there is an newer alternative for ITSx that uses fastq (instead of fasta) and should be better suitable for ASVs, according to their description. Is there any plan to support ITSxpress?

Thank you

a-h-b commented 1 year ago

Hi - I think we can include this in a future version. In the meantime, I am not super-convinced that it will improve results greatly... if you run a normal ITS-configured dadasnake run, it will make ASVs and then you can filter/cut those (using iTSx). You can post-cluster them using vsearch (at 100% if you wish), so that should lead to 100%-OTUs over the ITS region of your choice. Maybe it's a bit more efficient with ITSexpress and I certainly like to have the choice of before or after ASV-construction, but it shouldn't make a huge difference. One thing to note however, is that I've seen examples of fungal ITS2 that were not recognized by ITSx, so I tend to double-check negative ITSx results anyway. Hope this helps - AHB