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Description

Simplifier is a stand-alone software that selectively eliminates redundant sequences from the collection of contigs generated by ab initio assembly of genomes. The software was implemented in JAVA (http://www.java.sun.com) utilizing the Swing library. The parallel processing was carried out with the use of threads, to improve the performance of the software.

Requirements

Sun jdk 6 or higher

Table of Parameters

Parameter Description
-i Multifasta file containg contigs
-c How many bases at the ends can be disregarded for the identification of redundant sequence
-o Output file which will containing the set of contigs without redundant sequences

Command line

java -jar Simplifier.jar -i <input file > -c <number of bases to be trimmed> -o <output file>

Download

From SourceForge

From UFPA

Contact

Prof. Rommel Ramos - rommelramos@ufpa.br

Prof. Artur Silva -asilva@ufpa.br