Whole-genome sequencing data analysis software tools

Whole genome sequencing (WGS) is the next-generation sequencing technology for a rapid and low cost determining of the full genomic sequence of an organism. Deep sequencing of genomes is important not only to improve our knowledge in life sciences and evolutionary biology but also to make clinical progresses. Interpreting WGS data and understanding the importance of genomic variants in health and disease (see genome-wide association analysis, GWAS) represent the cornerstone of the precision medicine initiative. The WGS analysis workflow includes data processing and quality control, here the tools are mostly common to all NGS data analyses. Specific tools are then required for genotyping, for identifying somatic and germline mutations, indel, CNV, structural variation and repetitive DNA elements. Thus, variant annotation, data visualization and interpretation can be performed using dedicated databases and software tools. Platforms are also proposed for data management as well as pipelines to support complex WGS analysis.

Data preprocessing

Data processing

Data analysis

Genome variant analysis


Variant effect analysis

Genome-wide association study/Linkage/QTL


Population genetic analysis

Virus genome analysis

Data visualization

Network analysis


File manipulation


Unclassified tools