rRNA identification and removal.
Easy identification and removal
of rRNA-like sequences.
The riboPicker tool can be used to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic and metagenomic datasets. It is easily configurable and provides a user-friendly interface.
Input interface
The user can upload FASTA or FASTQ files and select the databases used for rRNA identification, including SILVA, RDP-II, Greengenes, Rfam, HMP genomes, and NCBI archaeal/bacterial genomes.
Interactive result selection
The user can set the thresholds interactively and see the results directly using the functionality of the graphical interface. The results and additional information can then be easily downloaded.
Coverage plots
The coverage plots provide additional information that can guide the selections of the thresholds and identify possible bias or contamination in the dataset.
News and Updates
Here you will find release notes and news related to riboPicker.
02 / 2012
Database updates: The non-redundant database for the standalone version is now additionally available through FTP at ftp://edwards.sdsu.edu:7009/ribopicker/db/. Added a human rRNA database to the web interface.
Documentation updates: The documentation for the human rRNA database was added to the Manual section.
01 / 2012
Database updates: SILVA (108), RDP-II (Release 10, Update 28), HMP reference genomes (20111206), and NCBI archaeal/bacterial complete genomes (20120117) were updated for the web-interface. The latest version of the non-redundant database for the standalone version is available at http://edwards.sdsu.edu/ribopicker/rrnadb/rrnadb_2012-01-17.tar.gz
Documentation updates: The documentation for each rRNA database was added to the Manual section and includes detailed steps on how to create each of the databases for use with the standalone version.
12 / 2011
Release of version 0.4.3: Extended documentation and help. Added example data to the standalone version.
10 / 2011
Release of version 0.4.2: Extended the input format from ACGTN to full nucleic acid ambiguity code (ACGTURYKMSWBDHVNX-). Added FASTQ input support (standalone). Added FindBin (and alternatives) to standalone version to prevent issues when runnning the tool from a different directory.
Database updates: RDP-II (Release 10, Update 27), HMP reference genomes (20110912), and NCBI archaeal/bacterial complete genomes (20111016) were updated for the web-interface. The latest version of the non-redundant database for the standalone version is available at http://edwards.sdsu.edu/ribopicker/rrnadb/rrnadb_2011-10-16.tar.gz
09 / 2011
Release of version 0.4: Allow to filter results by alignment length in addition to the coverage and identity thresholds.
08 / 2011
Release of version 0.3: Enhanced interface with additional information of results (domain and phyla by database). Extended FAQ and Manual sites on sourceforge. Added and updated databases.
Release of standalone version: With release 0.3, riboPicker is now available as standalone version for offline use and/or integration into your processing pipeline.
07 / 2011
Release of version 0.2: Added coverage plot generation that allows plot updating based on current threshold values. Added coverage values output file to output selection.
03 / 2011
Release of version 0.1: First public release of riboPicker.