How to improve taxonomic classification resolution of 16S rDNA, nanopore sequencing?

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I’ve been learning to process my 16S rDNA nanopore sequences with the Galaxy workflow from the tutorial “16S Microbial analysis with Nanopore data” (the data in the tutorial is corrupted by the way).

The sequences I have are from a synthetic community standard, so I know what to look for and at what abundances. Another member of my group has analysed this data with a non-galaxy approach and was able to get genus-level information.

My results have been very low resolution in comparison. I have tried Kraken2 with different databases as reference, but would love some help or ideas as to how I could improve my results, ideally to as many genus classifications as possible, or family. Anything would be helpful!!!

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Hi @Lid,
currently, we are working on a new tool for that goal Add PathoScope by gallardoalba · Pull Request #1212 · bgruening/galaxytools · GitHub, however, is still not available. It would be great if you could provide me with some details about the pipeline that your colleague followed since it could be useful for us in order to improve the training material.

Best regards

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Hello,

Unfortunately my colleague used EPI2ME, which is opaque. This is why I am looking into other methods, and they are as well. But great to know there is development about this, sorry I can’t be of more help!

Lydia

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