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Viola: a structural variant signature extractor with user-defined classifications
Bioinformatics ( IF 5.8 ) Pub Date : 2021-09-14 , DOI: 10.1093/bioinformatics/btab662
Itsuki Sugita 1, 2 , Shohei Matsuyama 2 , Hiroki Dobashi 2 , Daisuke Komura 1 , Shumpei Ishikawa 1
Affiliation  

Summary Here, we present Viola, a Python package that provides structural variant (SV; large scale genome DNA variations that can result in disease, e.g. cancer) signature analytical functions and utilities for custom SV classification, merging multi-SV-caller output files and SV annotation. We demonstrate that Viola can extract biologically meaningful SV signatures from publicly available SV data for cancer and we evaluate the computational time necessary for annotation of the data. Availability and implementation Viola is available on pip (https://pypi.org/project/Viola-SV/) and the source code is on GitHub (https://github.com/dermasugita/Viola-SV). Supplementary information Supplementary data are available at Bioinformatics online.

中文翻译:

Viola:具有用户定义分类的结构变体签名提取器

总结在这里,我们介绍了 Viola,这是一个 Python 包,它提供结构变体(SV;可导致疾病,例如癌症的大规模基因组 DNA 变异)特征分析函数和用于自定义 SV 分类的实用程序,合并多 SV 调用者输出文件和SV 注释。我们证明 Viola 可以从公开可用的癌症 SV 数据中提取具有生物学意义的 SV 签名,并且我们评估了注释数据所需的计算时间。可用性和实施​​ Viola 在 pip (https://pypi.org/project/Viola-SV/) 上可用,源代码在 GitHub (https://github.com/dermasugita/Viola-SV) 上。补充信息 补充数据可在 Bioinformatics 在线获取。
更新日期:2021-09-14
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