Software for chimera detection of amplicon (e.g. 16S) nanopore reads
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9 weeks ago
rob_DNA ▴ 20


does anyone have experience with detecting (PCR) chimeras based on a reference database using amplicon data of whole bacterial/fungal/.. communities? For example, 16S amplicons of soil bacterial communities.

what I've tried/found so far:

1) I've tried vsearch --uchime_ref, but as vsearch --uchime_ref is developped for accurate short-reads, I think it does not perform well on nanopore reads of ~1500 bp in length.

2) There is a program called yacrd ( but this is not developed or optimized for amplicon data, as stated by the developer.

3) PoreChop should also be able to detect chimeras, but because it is unsupported for quite a while now, I'd rather not use it.

4) ChimeraBuster, but this is developped for genomoc/transcript chimera detection, and not for amplicon.

Any ideas? Thanks!

chimera nanopore amplicon • 197 views

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