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Updated: May 26, 2026

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples
Published on: December 22, 2014
Identification and removal of ribosomal RNA sequences from metatranscriptomes
Robert Schmieder1, Yan Wei Lim, Robert Edwards
1Department of Computer Science, San Diego State University, San Diego, CA 92182, USA. rschmied@sciences.sdsu.edu
Summary:
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.
Availability And Implementation:
This open-source application was implemented in Perl and can be used as stand-alone version or accessed online through a user-friendly web interface. The source code, user help and additional information is available at http://ribopicker.sourceforge.net/.
Contact:
rschmied@sciences.sdsu.edu; rschmied@sciences.sdsu.edu
Supplementary Information:
Supplementary data are available at Bioinformatics online.
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