CoVaCS

CoVaCS is a software tool that has been designed to address the need for accurate and time-effective bioinformatics systems for genotyping in the field of personalized genomics and precision medicine. With the rapid increase in the rate of human genome re-sequencing data due to the advent and ongoing development of next-generation sequencing (NGS) technologies, the body of genome re-sequencing data is progressively increasing, and the need for accurate and efficient bioinformatics tools is becoming more significant.

CoVaCS is a fully automated, web-based system that integrates state-of-the-art tools for variant calling and annotation for whole genome sequencing (WGS), whole-exome sequencing (WES), and target-gene sequencing (TGS) data. This system offers optimized pipelines that provide accurate and reliable genotyping and variant annotation.

Extensive tests conducted on a gold standard benchmark dataset, the NA12878 Illumina platinum genome, confirm that call sets based on CoVaCS's consensus strategy are completely in line with those attained by similar command-line-based approaches. Furthermore, call sets produced by CoVaCS are more accurate than those produced by any individual tool, and the system exhibits better sensitivity and higher specificity than equivalent commercial software.

CoVaCS is hosted at Cineca and offers the speed of a High-Performance Computing (HPC) facility, which is crucial when large numbers of samples must be analyzed. Moreover, all analyses are performed automatically, allowing for high reproducibility of the results.