RiboPicker

Application data
Created by	Robert Schmieder
Biological application domain(s)	Transcriptomics, Metagenomics, Genomics
Principal bioinformatics method(s)	Read pre-processing, rRNA filtering
Technology	Sanger, Illumina, 454, Ion Torrent, PacBio
Created at	San Diego State University, Sourceforge
Maintained?	Yes
Input format(s)	FASTA, FASTQ
Output format(s)	FASTA, FASTQ
Programming language(s)	Perl, C
Licence	GPLv3
Operating system(s)	UNIX, Mac OS X

Summary: riboPicker is a publicly available tool that is able to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic and metagenomic datasets. riboPicker is available as both standalone and web-based versions.

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Description

The majority of RNA recovered in metatranscriptomic studies is ribosomal RNA (rRNA), not mRNA, often exceeding 90% of the total reads (Stewart et al., 2010; doi:10.1038/ismej.2010.18). Even after various treatments prior to sequencing, the observed rRNA content decreases only slightly (Hei et al., 2010; doi:10.1038/nmeth.1507). It is estimated that misannotations of rRNA as proteins may cause up to 90% false positive matches of rRNA-like sequences in metatranscriptomic studies (Tripp et al., 2011; doi:10.1093/nar/gkr576). Those false positive matches are a serious concern for downstream analysis, possibly causing erroneous conclusions. Therefore, the removal of rRNA-like sequences presents a necessary step for all metatranscriptomic projects.