ArticleJournal of computational biology : a journal of computational molecular cell biology2017
rRNAFilter: A Fast Approach for Ribosomal RNA Read Removal Without a Reference Database.
Article in Journal of computational biology : a journal of computational molecular cell biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- The potential role of short internodes/stylish (SHI/STY) and SHI related sequence (SRS) in potato tuberization.BMC plant biology · 2025Article
- Bioinformatic approaches to blood and tissue microbiome analyses: challenges and perspectives.Briefings in bioinformatics · 2025Review
- Rapid and accurate identification of ribosomal RNA sequences via deep learning.Nucleic acids research · 2022Article
- RelB contributes to the survival, migration and lymphomagenesis of B cells with constitutively active CD40 signaling.Frontiers in immunology · 2022Article
- ZWA: Viral genome assembly and characterization hindrances from virus-host chimeric reads; a refining approach.PLoS computational biology · 2021Article
- mixtureS: a novel tool for bacterial strain genome reconstruction from reads.Bioinformatics (Oxford, England) · 2021Article
- Article
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Authors and funding
3 authors.
Funding
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Abstract
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.
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