Identification and removal of ribosomal RNA sequences from metatranscriptomes

Robert Schmieder; Yan Wei Lim; Robert Edwards

doi:10.1093/bioinformatics/btr669

Identification and removal of ribosomal RNA sequences from metatranscriptomes

Robert Schmieder
, Yan Wei Lim
, Robert Edwards

Research output: Contribution to journal › Article › peer-review

183 Citations (Scopus)

35 Downloads (Pure)

Abstract

Here, we present riboPicker, a robust framework for the rapid, automated identification and removal of ribosomal RNA sequences from metatranscriptomic datasets. The results can be exported for subsequent analysis, and the databases used for the web-based version are updated on a regular basis. riboPicker categorizes rRNA-like sequences and provides graphical visualizations and tabular outputs of ribosomal coverage, alignment results and taxonomic classifications.

Original language	English
Article number	btr669
Pages (from-to)	433-435
Number of pages	3
Journal	Bioinformatics
Volume	28
Issue number	3
DOIs	https://doi.org/10.1093/bioinformatics/btr669
Publication status	Published - 1 Feb 2012
Externally published	Yes

Bibliographical note

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited

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Edwards_Identification_P2012Final published version, 96.6 KBLicence: CC BY-NC

Cite this

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N2 - Here, we present riboPicker, a robust framework for the rapid, automated identification and removal of ribosomal RNA sequences from metatranscriptomic datasets. The results can be exported for subsequent analysis, and the databases used for the web-based version are updated on a regular basis. riboPicker categorizes rRNA-like sequences and provides graphical visualizations and tabular outputs of ribosomal coverage, alignment results and taxonomic classifications.

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Identification and removal of ribosomal RNA sequences from metatranscriptomes

Abstract

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