RiboPicker
Application data |
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Created by | Robert Schmieder |
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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.
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