Development of a software package for the analysis of genome resequencing data in aquatic populations

In recent decades, genome resequencing has been widely applied to study the genetic diversity in wild populations or cultured populations, such as estimation of divergence of populations and detection of artificial or environmental selection on the chromosomes. However, owing to lack of bioinformatics skills, most of the researchers have to resort to commercial platforms to analyze resequencing data, which needs high costs and long analysis period. The commercial platforms usually use the universal pipelines without personalized analysis, which sometime causes the erroneous results due to unreasonable parameters or reference genome data. Owing to the increasing demands of genome resequence data analysis in aquatic animals, we developed a user-friendly software package to facilitate population genetics analysis of genome resequencing data for aquatic biologists who may lack bioinformatics skills. By surveying the current research and achievements in the analysis of resequencing data in aquatic animals, the constructed software package integrated different bioinformatic tools, encompassing mapping the quality-controlled reads to the reference genome, detecting genetic variations, performing phylogeny and principal component analysis, clarifying population structure, calculating quantitative indicators of genetic diversity, and completing selective sweep analysis. All of the resulting data were finally visualized with an R or a Python language package. The present package was tested by analyzing the resequencing data of 30 Larimichthys crocea individuals of 3 populations, which successfully completed all of the designed tasks, such as alignment of the reads, identification of single nucleotide polymorphism (SNP), construction of phylogenetic tree and population structure, illustration of linkage disequilibrium decay and calculation of main diversity indexes. The generated outputs were well-visualized. The software package functionally integrated most of the basic statistics, calculation, and plotting for the analysis of wild and natural populations, which enabled most of the researchers to locally perform the data mining of genome resequence data to save time and costs. The corresponding source codes and instruction manuals have been uploaded to GitHub: https://github.com/xqteng/Re-seq_analysis.