We have released a major update to ClinDet. As a result, this repository is no longer actively maintained. For the latest version, please visit the new GitHub repository for details.

clindet is a fully automated multi-omics data analysis pipeline based on Snakemake and singularity. This pipeline enables the analysis of multi-omics data from thousands of patients in cancer cohorts. It can analyze whole-genome, whole-exome, and transcriptome data, and perform commonly used clinical tasks such as gene mutation detection, structural and copy number variation detection, and transcript quantification and fusion gene detection analysis.

• scRNA-seq, scATAC-seq analysis workflow
• Mutational signature analysis, driver genes detection,...
• human T2T genome reference support
• ......