An Integrated Bioinformatics Framework for Genomic Variants Discovery from Next Generation Sequencing Data

Next Generation Sequencing (NGS) technologies have increased exponentially the understanding of the genomic structure and function of different organisms within the last decade, including the CIAT mandate crops. In order to handle the vast amount of data produced by these technologies, several bioinformatic tools have been developed to carry on different kinds of analysis. However, most of these tools are not easy to operate, integrate and customize without the technical support of experts in bioinformatics, which produces a bottleneck for several research efforts. This situation poses the need for integrated data analysis pipelines with user friendly interfaces available to the scientific community.

We have developed NGSEP (NGSTools Eclipse Pluging), an integrated framework for variants discovery from NGS data. NGSEP is based on Eclipse which is one of the leading development environments for Java. We integrated previously developed algorithms for SNV detection available in the NGSTools package with Java implementations of state-of-the-art algorithms for CNV and structural variation discovery. NGSEP provides an intuitive interface in which the user has a rich control over the files produced during the different stages of the analysis. These files follow current standard formats such as BAM and VCF, which makes NGSEP results easy to integrate with genome visualization tools. NGSEP can also be integrated with bowtie2 to allow the user to follow all the steps needed to obtain genomic variants from raw reads without scripting. NGSEP will be distributed as an open source project under GPL license to make it available to the scientific community.