Arapan Assembler Files

Argan 1.0.0

Argan is an artificial sequencing tool. 
Argan is a command-line tool that tends to be 
standard software for simulating artificial data 
from complete genomes. The structure of this tool
consists of a Sequencer and an Errorizor.

STRUCTURE
---------
Argan was designed in such a manner that it could 
produce short reads of the same length. 
The first task that should be done by Argan sequencer 
is to determine the reverse complement of the genome. 
The rest of the algorithm is divided into two main phases: 
Sequencer and Errorizor.

1. Sequencer
Two parameters control the sequencer: the coverage C and 
the length of short reads L. The algorithm starts from the 
head of the genome; it creates short reads by randomly 
choosing either the genome or its reverse complement.

2. Errorisor
After generating reads, the Errorizer will be automatically 
invoked. It converts the errors rate E to the number of 
maximal authorized reads M that should include errors. 
The Errorizor algorithm also requires two parameters: 
the length of short reads L and the error rate E.


INSTALLATION
------------

Qt libraries must be installed.
It can be downloaded from (http://qt.nokia.com/downloads)

To compile Argan, simply run:

make


RUNNING ARGAN
-------------
Syntax: 

 ./Argan input ouput L C E

such that:
   L = Length of reads (e.g. 35,40,60,100...) 7 < L < genome size
   C = Coverage
   E = Error rates (0.5, 0.6, 1, 1.5, 2, 3 ...)


ACKNOWLEDGMENTS
---------------
Mohammed Sahli, Tetsuo Shibuya

This work was partially supported by the Grant-in-Aid from the Ministry 
of Education, Culture, Sports, Science and Technology of Japan.


CONTACT
-------
Mohammed Sahli: mohammed@hgc.jp
Tetsuo Shibuya: tshibuya@hgc.jp