rRNAFilter: A Fast Approach for Ribosomal RNA Read Removal Without a Reference Database.

Metatranscriptomics studies the transcriptome of all microbial species in a habitat. Removing ribosomal RNA (rRNA) reads in metatranscriptomic data is essential for the study of microbial gene expression. Although several methods are developed, all of them rely on rRNA databases that contain a limited number of known rRNA sequences and cannot work well on rRNA reads from unknown rRNA sequences. To address this problem, we have developed a novel approach called rRNAFilter. Our method can accurately and rapidly remove rRNA reads from metatranscriptomes without any prior knowledge of known rRNA sequences. Compared with two existing approaches, rRNAFilter has shown comparable performance when working on reads from known rRNA sequences and much better performance when dealing with reads from unknown rRNA sequences.