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riboPicker ========== Identification and removal of rRNA-like sequences using a modified version of BWA-SW (http://ribopicker.sourceforge.net). For more information about BWA-SW go to http://bio-bwa.sourceforge.net/ To test the program, please read README_test.txt SETUP ----- 1. Create the databases used for rRNA screening Use command: bwaXXX index -p database_name fasta_file_with_rrna_references >out.txt 2>&1 & ("XXX" should be replaced by "MAC" or "64" based on your system architecture) For alternative system architectures, download BWA version 0.5.9 source code from http://bio-bwa.sourceforge.net/ (http://sourceforge.net/projects/bio-bwa/files/bwa-0.5.9.tar.bz2/download); extract the file with "tar -xjf bwa-0.5.9.tar.bz2"; replace files in the extracted BWA directory with the files in bwasw_modified_source (distributed with riboPicker); run "make" in the BWA directory. Notes: (i) It is advised to remove very short or long sequences from files retrieved from public resources. Most likely, those sequences are a result of misannotations and should not be included in the database. (ii) Removing duplicates may reduce the database size and speed up analysis. Tools such as PRINSEQ (http://prinseq.sourceforge.net/) can assist with this task. (iii) There seem to be some issues with Mac OSX 10.6.8 that will require you to compile the program (the bwaMAC version might crash). (iv) The non-redundant rRNA database can be downloaded from: http://edwards.sdsu.edu/ribopicker/rrnadb/ 2. Change values in riboPickerConfig.pm (if applicable) DB_DIR PROG_NAME PROG_DIR DBS DBS_DEFAULT Notes: (i) If the bwaXXX program is located in the same directory as the ribopicker.pl file, please specify ./ as program directory (use constant PROG_DIR => './';). USAGE ----- Run as: perl ribopicker.pl [options] -f <file> -dbs <list> ... or rename file and set chmod +x to run as: ./ribopicker [options] -f <file> -dbs <list> ... Try 'ribopicker -h' for more information on the options. DEPENDENCIES ------------ The PERL script requires these other modules: riboPickerConfig (included) Data::Dumper Getopt::Long Pod::Usage File::Path >= 2.07 Cwd FindBin Note: If you do not like to use FindBin, replace the FindBin module with either of: A File::Basename + Cwd version: use File::Basename qw(dirname); use Cwd qw(abs_path); use lib dirname(abs_path($0)); A File::Basename + File::Spec version: use File::Basename qw(dirname); use File::Spec; use lib dirname(File::Spec->rel2abs($0)); BUG REPORTS ----------- If you find a bug please email me at <rschmieder_at_gmail_dot_com> or report a bug at http://sourceforge.net/p/ribopicker/bugs/ so that I can make riboPicker better. COPYRIGHT AND LICENSE --------------------- Copyright (C) 2011 Robert SCHMIEDER This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>. VERSION HISTORY --------------- (If not otherwise stated, changes apply to the standalone and web version after version 0.3.) ribopicker-0.4.3: Extended documentation and help. Added example data to the standalone version. ribopicker-0.4.2: Added FindBin (and alternatives) to standalone version to prevent issues when runnning the tool from a different directory. ribopicker-0.4.1: Extended the input format from ACGTN to full nucleic acid ambiguity code (ACGTURYKMSWBDHVNX-). Added FASTQ input support (standalone). ribopicker-0.4: Allow to filter results by alignment length in addition to the coverage and identity thresholds. ribopicker-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. With release 0.3, riboPicker is now available as standalone version for offline use and/or integration into your processing pipeline. ribopicker-0.2: Added coverage plot generation that allows plot updating based on current threshold values. Added coverage values output file to output selection. ribopicker-0.1: First public release of riboPicker.