Metagenomics produces a taxonomical profile of the sample, metatranscriptomics helps us to obtain a functional profile. rRNAFilter is a novel taxonomy-independent approach which can accurately and rapidly filter rRNA sequences from metatranscirptomes without the aid of reference rRNA databases. It not only has comparable accuracy with current similarity-based methods, but also much faster than these methods.


Software Version
rRNAFilter V1.1


We just need to input reads in fasta format from metatranscirptomes to run rRNAFilter:

There are two modes to run rRNAFilter:
  • rRNAFilter_m1:filter rRNA reads confidently, and leave a small number of reads unfiltered.
  • rRNAFilter_m2:filter all rRNA reads (default option)


rRNAFilter filter rRNA reads from metatranscriptomic data. It will output two files which contain rRNA reads and non-rRNA reads separately. See manual for the details of how to use rRNAFilter.

For any questions, please contact us with emails:
  • Ying Wang:
  • Haiyan Hu:
  • Xiaoman Li: