DIVIS: Integrated and Customizable Pipeline for Cancer Genome Sequencing Analysis and Interpretation

• Published in: Frontiers in oncology Vol. 11; p. 672597
• Main Authors: He, Xiaoyu, Zhang, Yu, Yuan, Danyang, Han, Xinyin, He, Jiayin, Duan, Xiaohong, Liu, Siyao, Wang, Xintong, Niu, Beifang
• Format: Journal Article
• Language: English
• Published: Frontiers Media S.A 08-06-2021
• Subjects: cancer; customization; next-generation sequencing; Oncology; variants detection; workflow
• ISSN: 2234-943X; 2234-943X
• DOI: 10.3389/fonc.2021.672597

Next-generation sequencing (NGS) has drastically enhanced human cancer research, but diverse sequencing strategies, complicated open-source software, and the identification of massive numbers of mutations have limited the clinical application of NGS. Here, we first presented GPyFlow, a lightweight tool that flexibly customizes, executes, and shares workflows. We then introduced DIVIS, a customizable pipeline based on GPyFlow that integrates read preprocessing, alignment, variant detection, and annotation of whole-genome sequencing, whole-exome sequencing, and gene-panel sequencing. By default, DIVIS screens variants from multiple callers and generates a standard variant-detection format list containing caller evidence for each sample, which is compatible with advanced analyses. Lastly, DIVIS generates a statistical report, including command lines, parameters, quality-control indicators, and mutation summary. DIVIS substantially facilitates complex cancer genome sequencing analyses by means of a single powerful and easy-to-use command. The DIVIS code is freely available at
https://github.com/niu-lab/DIVIS
, and the docker image can be downloaded from
https://hub.docker.com/repository/docker/sunshinerain/divis
.