Biological Expression Network Data Integration

Abstract

Next Generation Sequencing (NGS), as the most popular sequencing method, has an exponential growth amount of publication focused on this area for the recent twenty years. It can help researchers reveal the polymorphism of DNA sequences on the whole genome scale for diverse species, and hence provides us an unprecedented opportunity to analyze population characteristics. However, the lack of systematical tools with proper software structure poses a practical obstacle to tackle such a large amount of data. To address this issue, I have developed a toolkit called NGS toolkit following with software design principle, which is the first comprehensive software package incorporating popular algorithms and statistical measures, for NGS population genetics analysis. The package consists of seven modules: format transformation, haplotype analysis, linkage disequilibrium evaluation, phylogenetic tree construction, population structure inference, introgression and positive selection.