Comments (5)
Thanks!
The idea here could be to add a parameter, e.g. --contamination_controls "sample1,sample2"
, and all sequences that appear in that control samples are removed from the ASV table (including the control samples itself).
More advanced for such a task (using control samples) might be decontam which is also in bioconda.
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I would absolutely recommend Decontam. We have seen in actual projects that raw removal of ASVs found in negative controls risks both to remove true ASVs found in samples and miss contaminants. This is, of course, taking Decontam as the truth, but the results have looked intuitively good.
There are at least two ways of running Decontam, and I think it would be wise to allow both.
from ampliseq.
Alright, thanks, then it will be not worth the effort to implement the simple method above but rather immediately a proper one such as Decontam.
from ampliseq.
Hi all,
I wouldn't advise decontam until everything is known about how it removes an asv - exactly. We still need a clean feature which will simply remove anything in the control samples as a first pass for comparison with a second pass without removal. This is what we did before ampliseq and what most microbiologists do with every project - scan the controls and remove what they see as a legitimate contamination. To do this removal is time intensive and tedious and then you have to replot. It would be truly worthwhile to have this feature as an option, then we can look at the output and decide if it's worth using decontam instead or not. It certainly should be an option as it currently is not an option in decontam!
from ampliseq.
Hm thats a rather emotional plea for a simple method. I do think that the decontam documentation is not too ambiguous. Decontam implements a method that is using control samples, see here, I am not sure what your exact criticism is?
Manual manipulation is however the worst way of data processing in my opinion, it would be in any case better to automatize, i.e. standardize and make reproducible. I can live with having optional filters available. If you or someone else wants to implements that simple method because you feel its a method with future, I will not stand in your way (I cannot speak for others though).
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Related Issues (20)
- Phyloseq object creation will fail if any samples have all reads removed by the tax filtering step HOT 5
- Add blast-consensus support to Ampliseq HOT 1
- Add greengenes2 2022.10 support to Ampliseq HOT 1
- Add custom qiime reference database support to Ampliseq. HOT 2
- Edge case: Clustering with VSEARCH fails at QIIME2_INSEQ HOT 1
- Allow to analyse 454 sequencing data HOT 2
- Add option to assign ASV to multiple species with DADA2 HOT 3
- Debug information for docker-based run. HOT 4
- Allow stratified output from picrust2 HOT 4
- nf-core/ampliseq with conda - change bioconductor-biostrings HOT 2
- Launch webpage not working HOT 4
- Adding qza file for downstream analysis in R HOT 3
- When using `--vsearch_cluster`, if you have many thousands of clusters, `AMPLISEQ:FILTER_CLUSTERS` will fail with an `Argument list too long` error. HOT 8
- test_full Cannot access file fastq HOT 1
- Multipe region amplicon sequencing analysis support (5R / SMURF / q2-sidle) HOT 1
- Getting ca 50% more ASVs than when using DADA2 on QIIME2 HOT 2
- ampliseq fails during taxonomy assignation when processing ITS sequences HOT 14
- Error No subject alternative DNS name matching zenodo.org found HOT 2
- minor improvement of sort() before denoising with method = "radix HOT 2
- 12S taxonomic classification databases HOT 3
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