kataegis: an R package for identification and visualization of the genomic localized hypermutation regions using high-throughput sequencing

BMC Genomics

Xue Lin¹  Peng Dai¹  Jian Li²  Pin Chen²  Shuanglin Gu²  Li Lv²  Yunyun Hu²  Xingyu Li²  Anna Liu²  Yingying Hua³ 

[1] Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, 211166, Nanjing, People’s Republic of China;Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, 210096, Nanjing, People’s Republic of China;Traditional Chinese Medicine Department, Fuxing Hospital, Capital Medical University, 100038, Beijing, People’s Republic of China;

关键词: Kataegis;    Visualization;    High-throughput sequencing;    R;   

DOI  :  10.1186/s12864-021-07696-x

来源: Springer

【 摘 要 】

BackgroundGenomic localized hypermutation regions were found in cancers, which were reported to be related to the prognosis of cancers. This genomic localized hypermutation is quite different from the usual somatic mutations in the frequency of occurrence and genomic density. It is like a mutations “violent storm”, which is just what the Greek word “kataegis” means.ResultsThere are needs for a light-weighted and simple-to-use toolkit to identify and visualize the localized hypermutation regions in genome. Thus we developed the R package “kataegis” to meet these needs. The package used only three steps to identify the genomic hypermutation regions, i.e., i) read in the variation files in standard formats; ii) calculate the inter-mutational distances; iii) identify the hypermutation regions with appropriate parameters, and finally one step to visualize the nucleotide contents and spectra of both the foci and flanking regions, and the genomic landscape of these regions.ConclusionsThe kataegis package is available on Bionconductor/Github (https://github.com/flosalbizziae/kataegis), which provides a light-weighted and simple-to-use toolkit for quickly identifying and visualizing the genomic hypermuation regions.

【 授权许可】

CC BY