AREOS - a Repeat Element Oriented Short Read Simulator

Assembling complex genomes remains a great challenge due to the short reads that are actually produced by the next-generation sequencing (NGS) technologies. However, the main obstacle in assembly processes is to deal with a high content of repeated sequences. So far, no controlled environment that takes into account repeated sequences was available to assist assembler programs. Simulated data is indispensable for guiding tool development and evaluating tool performance, and therefore it is essential to develop simulation software that can produce next-generation sequencing read sets that captures the most essential characteristics of true genome data. Here we present AREOS, a program that simulates a genome reference sequence with insertions of repetitive sequences such as TEs and then, generates simulated short reads similar to those produced by the Solexa/Illumina platform.  We propose a useful tool that will aid in evaluating and comparing assemblies by analyzing how the assembly programs overcome the presence of repeated sequences in a complex sequenced genome. AREOS is a powerful tool to test NGS assemblers against complex genomes enriched with TEs. AEROS will also be useful in the development of future assemblers that will improve on the repeat sequencing assembly. AREOS is implemented in PERL, and requires BioPerl as well as the Math::Random library installed.