Closed hoelzer closed 2 years ago
yeah makes sense to add this i think. feel free to do a PR :)
Hi there, I'm on it and I was just wondering:
kraken2
just classifies the reads, right? The not-SARS-CoV-2 reads are not filtered out and the reconstruction is done on the whole set of reads (fastq_input_ch
)? (see https://github.com/replikation/poreCov/blob/master/poreCov.nf#L355-L368)
Yes, that's the read length filter. But what about the reads that are not classified as SARS-CoV-2. They are also used in the reconstruction, right?
So it's not: kraken2 -> take only SARS-CoV-2 reads -> reconstruction
Edit: I think above was a 'not' missing, sorry
Okay - just doublechecking :)
Yes exactly. It's actually a bit different to other approaches (e.g. covpipe @Marie) where people just continue with the set of sequences that was classified as SC2. But what if the ref db gets outdated (looking at you Delta...)
Honestly, I also think it makes not much difference especially for long reads. The reads are anyway mapped to the (Wuhan) reference then and a 400 nt human read will not map. Thus, we just added kraken2 on top to the general artic workflow to have these classification/contamination counts in the report but still throw all the reads into the artic workflow.
But good you double checked, and thx that you are looking into it already! ;)
On Tue, 9 Nov 2021, 18:11 MarieLataretu, @.***> wrote:
Okay - just doublechecking :)
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also kraken2 (as it needs more RAM) can fail in poreCov on low end computers, without compromising the whole pipeline and the user still gets a genome assembly + lineage
Hi,
this just popped up based on a recent run:
kraken2
found here ~900 reads assigned to SARS-CoV-2 from a negative controlAlso, if we just
minimp2
the NC reads (unfiltered) to SARS-CoV-2 we hardly get any hit.Thus, it seems that some "junk" is just assigned to SARS-CoV-2 via
kraken2
.It's also a bit confusing that later in the pipeline always the filtered read FASTQs are used but in the report the contamination percentages are based on the unfiltered files.
Thus, proposal: move the
kraken2
step after the length filter.What do you think? I can also help w/ the implementation change if you are fine w/ such an PR.