search

hildebra / lotus2

Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.
http://lotus2.earlham.ac.uk/
GNU General Public License v3.0
52 stars 17 forks source link

processing #68

Closed CFox-Lin closed 3 months ago

CFox-Lin commented 3 months ago

When I use RDPClassifier to annotate my fungi data, the program aborted with: ITS region was chosen as target; this requires a similarity based taxonomic annotation and excludes RDP tax annotation. Blast similarity based annotation is not possible due to: Similarity search was not explicitly activated (please use option "-taxAligner usearch" or vsearch,lambda,blast). However, RDPClassifier is able to process ITS data with --g [fungallsu|fungalits_warcup|fungalits_unite], will this be possible in future version? Thanks

hildebra commented 3 months ago

Hey, we never implemented this in LotuS2, therefore the warning so the user is aware that this currently can't be done. However, this looks like an easy enough implementation, we can have a look in the next weeks. best, Falk