The bioBakery help forum

Please update your ribosomal RNA depletion database

Dear KneadData users - We’ve just released an important update to KneadData’s SILVA-based database for depletion of microbial ribosomal sequences from metatranscriptomes. This update fixes a critical issue with U characters in the input sequences not being properly indexed by bowtie2 for downstream mapping.

The updated database file is available here. You can automatically update your local database using this command:

kneaddata_database --download ribosomal_RNA bowtie2 $DIR