Sigflow: an automated and comprehensive pipeline for cancer genome mutational signature analysis

Mutational signatures are recurring DNA alteration patterns caused by distinct mutational events during the evolution of cancer. In recent years, several bioinformatics tools are available for mutational signature analysis. However, most of them focus on specific type of mutation or have limited scope of application. A pipeline tool for comprehensive mutational signature analysis is still lacking. Here we present Sigflow pipeline, which provides an one-stop solution for de novo signature extraction, reference signature fitting, signature stability analysis, sample clustering based on signature exposure in different types of genome DNA alterations including single base substitution, doublet base substitution, small insertion and deletion and copy number alteration. A Docker image is constructed to solve the complex and time-consuming installation issues, and this enables reproducible research by version control of all dependent tools along with their environments. Sigflow pipeline can be applied to both human and mouse genomes.

Automated summary

Sigflow pipeline is a comprehensive tool for mutational signature analysis, allowing tasks such as de novo signature extraction, reference signature fitting, stability analysis, and sample clustering based on different types of genome DNA alterations, and it can be applied to both human and mouse genomes.