VISPA README (version 2.0)

UNIX Installation
------------------
1. Install MosaikAligner 2.1.73 software (see https://code.google.com/p/mosaik-aligner/downloads/list)
2. Create subfolder for ViSpA (for example, VISPA).
3. Unzip vispa02.zip from http://alan.cs.gsu.edu/NGS/?q=content/vispa
   into VISPA subfolder.


Running MOSAIK+VISPA
-------------------------------------

You can run wrapper bash script from VISPA folder as follows:

        nohup ./main_mosaik.bash <readFile> <referenceFile> threads n t &

or
        nohup ./main_mosaik.bash <readFile> <referenceFile> threads n t > <log> &


where
     - <readFile> is the absolute path to read file produced by 454 Life Sciences in fa format
     - <referenceFile> is the absolute path to file with reference (consensus) sequence in fa format
       NOTE: sequence should be in one line  
     - threads is the number of threads required for alignment in MOSAIK (usually, 12 is enough)
     - n is a number of mismatches allowed to cluster reads around superreads; 
       n is usually small integer in range [0,6]. The smaller genomic diversity 
       is expected, the smaller n value should be used. If reads are corrected by 
       ShoRAH, n is in the range [0,2].
     - t is a multation-based range over 5205bp region. Value of t depends on 
       expected underlying genomic diversity. In general, t varies over [80, 450]. 
       If reads are corrected by ShoRAH, t varies over range [0,20].
     - <log> is the absolute path to log file stored all outputs from the vispa program.

ViSpA outputs file starting with the name of read file and ending on EM20.txt that countains assembled quasispecies with their 
maximum-likelihood frequency estimation. 
Sequences are given in the descending order of their maximum-likelihood estimations. 
The format of the line is:
                <frequency>:<assembled sequence>	

Example:
./main_mosaik.bash /home/test/eps0.3_40reads.fa /home/test/population10_ref.fa 15 6 120 > /home/test/log.txt

The output is in /home/test/eps0.3_40reads_I_6_15_CNTGS_DIST0_EM20.txt


Source Code
-----------
The source code can be found at http://alan.cs.gsu.edu/NGS/?q=content/vispa

Revision history
----------------
Version 01 (3/11/11)  - first public release
Version 02

Contact
-------
For questions or suggestions regarding ViSpA you can contact:

     Irina Astrovskaya (iraa@cs.gsu.edu)
     Alex Zelikovsky (alexz@cs.gsu.edu)