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Add vsearch uchime_denovo for chimera removal (or flagging) #631
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Hi, The output from vsearch chimera detection is then used to filter out chimeric ASVs using different parameters such as
Let me know if you want to discuss this and how to implement it in ampliseq. |
Hi!
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
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.) |
Description of feature
We have found in deeply sequenced (1 M reads / sample) COI datasets that a lot of chimeras remain (0 - 15% of the ASVs are chimeras) after running through DADA2, including removeBimeraDenovo() with default settings. 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. Would be nice to have this as an option in nf-core/ampliseq. @johnne knows more about this.
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