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rRNAFilter V1.1 (June 2016)

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rRNAFilter is a novel taxonomy-independent approach which can accurately and rapidly filter rRNA 
sequences from metatranscirptomes without the aid of reference rRNA databases.

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1. Prerequisites

rRNAFilter can be run on Linux and Windows with Java and KAnalyze installed: 

** Java 
You need to install Java 7 and above version (64-bit is highly recommended). To check the 
version of the Java installed, please input the following command in the terminal:
	java -version

** KAnalyze
We use KAnalyze to do the k-mer counting. 

This tool was included in the software package.
Reference: Audano, Peter, and Fredrik Vannberg. "KAnalyze: a fast versatile pipelined K-mer 
toolkit." Bioinformatics 30.14 (2014): 2070-2072. 

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2. Input Parameters

We just need to input reads from metatranscirptomes to run rRNAFilter.

There are two modes to run rRNAFilter:
	1>rRNAFilter_m1: filter input reads confidently, and leave a small number of reads unfiltered.
    2>rRNAFilter_m2: filter all input reads (default option)
    

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3. Software Usage

We have both command line and GUI versions of rRNAFilter on Linux and Windows. 

(1) In terminal, use the following command to run rRNAFilter:
java -jar -XmxN rRNAFilter_commandline.jar -i reads_file -r 0 

	-XmxN(for example:-Xmx7g): Specify the maximum size of the memory allocation pool 
	for a Java Virtual Machine (JVM)
	-i (required) reads_file: reads file in FASTA format
	-r (optional) 0: filter all reads; 1: filter reads confidently, by default r=0
	
(2) We also provide GUI version of rRNAFilter, please refer to the manual to see what the GUI looks like.

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4. rRNAFilter Results

rRNAFilter will output two files: one file contains predicted rRNA reads and the other file contains predicted non-rRNA reads, the output file names are listed below:
	readsFile_rRNA
	readsFile_non-rRNA
	readsFile_non_filtered (if r=1, this is the group of unfiltered reads)

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* License
The rRNAFilter software is a freely available for academic use. 
It is also available for non-academic use under appropriate licensing.
Please contact Xiaoman Shawn li (xiaoman@mail.ucf.edu) for further information. 

*Contact info
If you are encountering any problem regarding to rRNAFilter, please refer the manual first.
If problem still cannot be solved, please feel free to contact us:
Ying Wang (ying2010@knights.ucf.edu)
Nancy Haiyan Hu (haihu@cs.ucf.edu)
Xiaoman Shawn Li (xiaoman@mail.ucf.edu)