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

Frontiers in Oncology

Xiaohong Duan¹  Siyao Liu¹  Xintong Wang¹  Jiayin He²  Yu Zhang³  Beifang Niu³  Xiaoyu He³  Danyang Yuan³  Xinyin Han³ 

[1] ChosenMed Technology (Beijing) Co., Ltd., Beijing, China;Computer Network Information Center, Chinese Academy of Sciences, Beijing, China;University of Chinese Academy of Sciences, Beijing, China;

关键词: variants detection;    customization;    workflow;    next-generation sequencing;    cancer;   

DOI  :  10.3389/fonc.2021.672597

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown