Daniel Straub
Daniel Straub
@benjjneb First of all, thanks for all your efforts with DADA2! I have added DADA2 as central building block to an amplicon analysis pipeline (https://nf-co.re/ampliseq & https://github.com/nf-core/ampliseq) and while developing...
Thanks for all the info! I did hear of DECIPHER:IdTaxa, but never looked deeper into it, I will do so!
If (in addition to rRNA removal as suggested in #227) an optional step would be added that would even remove all reads from a particular species, e.g. human, than this...
I am myself not involved in metagenomics of human samples but environmental samples, so my ideas have to be taken with a little caution. The simplest solution would be using...
Yes, you are right.
Interesting, do you have an example when that would be the case? To illustrate the problem. With what parameters would you cut the ASV sequences? Degenerated nucleotide sequence? Nucleotide positions?
So is this solved?
If using that container keyword works fine so far this seems to me as a valid option. However, that would need to be also working for conda & singularity, that...
> Is there a specific reason you're pulling singularity images from https://depot.galaxyproject.org/singularity/? I heard (never tried myself) that pulling docker images with singularity is more resource intensive and might be...
In the meantime - nf-core tools had an update --> nf-core linting fails in your fork (nf-core/ampliseq dev branch had its update and is passing) - nextflow had an update...