riboPicker is a tool to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic datasets. The tool was designed to process longer-read datasets (150+bp read length), but works on 100+bp reads too.
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Bioinformatics. 2012 Feb 1;28(3):433-5. Epub 2011 Dec 6.
Identification and removal of ribosomal RNA sequences from metatranscriptomes.
Schmieder R, Lim YW, Edwards R.