Introduction

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.

Publications

  1. rRNAFilter: A Fast Approach for Ribosomal RNA Read Removal Without a Reference Database.
    Cite this
    Wang Y, Hu H, Li X, 2017-04-01 - Journal of computational biology : a journal of computational molecular cell biology

Credits

  1. Ying Wang
    Developer

    1 Department of Computer Science, University of Central Florida

  2. Haiyan Hu
    Developer

    1 Department of Computer Science, University of Central Florida

  3. Xiaoman Li
    Investigator

    2 Burnett school of Biomedical Science, College of Medicine

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Summary
AccessionBT006483
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByXiaoman Li