Comments (2)
Hi,
Yes we implemented this additional chimera removal step via vsearch in this ASV-clustering workflow. See here in the Readme for an overview, and the relevant rules are in workflow/rules/chimeras.smk. Briefly, chimera detection is run either in 'batchwise' or 'samplewise' mode where the former runs the algorithm on ASVs found in all samples together, while the latter first splits the ASV input into one file per sample (based on ASV presence determined from a counts-file) then runs chimera detection on each of those file.
The output from vsearch chimera detection is then used to filter out chimeric ASVs using different parameters such as
- number/fraction of samples shared between chimera and parents
- number of samples in which an ASV has to be marked as chimeric
Let me know if you want to discuss this and how to implement it in ampliseq.
from ampliseq.
Hi!
Chimera removal is important, so I think this is indeed interesting.
Running uchime_denovo in vsearch seems to work well in removing remaining chimeric ASVs in our data (this allows for some mismatches between parents and children, which default removeBimeraDenovo does not) without removing "true" ASVs.
Yes, indeed default removeBimeraDenovo does not allow mismatches between chimera and parent, but using a config one could modify this behavior in ampliseq by overwriting that line, e.g. by using -c chimera.config
that contains
process {
withName: DADA2_RMCHIMERA {
ext.args = 'method="consensus", minSampleFraction = 0.9, ignoreNNegatives = 1, minFoldParentOverAbundance = 2, minParentAbundance = 8, allowOneOff = TRUE, minOneOffParentDistance = 4, maxShift = 16'
}
}
Would you be able to test whether that doesnt improve the chimera removal for your case in a similar manner? (Just want to make sure existing settings are not already covering this.)
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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
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