PVCTools: parallel variation calling tools

Jingjing Jin; Jiajun Liu; Yelin Yin; Zefeng Li; Peng Lu; Yalong Xu; Jianfeng Zhang; Peijian Cao; Dasha Hu

doi:10.1016/j.heliyon.2019.e02530

PVCTools: parallel variation calling tools

Heliyon. 2019 Oct 3;5(10):e02530. doi: 10.1016/j.heliyon.2019.e02530. eCollection 2019 Oct.

Authors

Jingjing Jin¹, Jiajun Liu², Yelin Yin³, Zefeng Li¹, Peng Lu¹, Yalong Xu¹, Jianfeng Zhang¹, Peijian Cao¹, Dasha Hu²

Affiliations

¹ China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China.
² Computer Science and Technology, Sichuan University, Chengdu, 450000, China.
³ Zhengzhou Tongbiao Environmental Testing Co., LTD, Zhengzhou, 450001, China.

Abstract

As the development of sequencing technology, it is now possible to sequence individuals of each species. Although a number of different tools have been developed to detect individual variations, most of them cannot be run in parallel modes. To accelerate variation detection, PVCTools is introduced in this study. PVCTools splits the reference genome and alignment files into small pieces and runs them in parallel mode. Meanwhile, boundary noise is also considered in PVCTools. From the result of three different sets of test data, PVCTools performs much faster than most other current tools. At the same time, it keeps similar accuracy with other tools. PVCTools is free and open source software. The development of sequencing technology and growing sample numbers will make performance improvements such as PVCTools increasingly interesting.

Keywords: Bioinformatics; Genetics; Parallel; Plant biology; Sequencing; Systems biology; Transcriptomics; Variation.