Fungi data

[goku830]

Description of feature

What are good parameters to use for fungi data. Is unite something good to use to classify fungi data because unite will not work for me .

[d4straub]

Why doesnt unite work for you? Maybe we can make it work?

[goku830]

I am running the nf-core/ampliseq pipeline with the --its2 flag and a UNITE reference database to analyze fungal ITS2 sequencing data, but the taxonomic classification output from DADA2 is only assigning reads at the kingdom level (e.g., “Eukaryota”) rather than providing deeper fungal taxonomy such as phylum, genus, or species names. Thisidentifying specific fungal taxa for differential abundance, suggests that the taxonomy reference may not be properly formatted for DADA2, that the UNITE training set being used is incompatible or incomplete, or that species-level assignment was not correctly enabled. As a result, the pipeline completes, but the classification resolution is too shallow to support

[d4straub]

Did you blast some of your ASVs to make sure that those are fine? I.e. that its not a data issue rather than a taxonomic classification issue.
You could also use a broader classification approach with -resume --skip_dada_taxonomy --kraken2_ref_taxonomy standard=20240904 as listed here to classify on genome sequences across kingdoms.