共识变异位点筛选软件——从全基因组测序数据到完整的变异列表。

ConsensuSV-from the whole-genome sequencing data to the complete variant list.

机构信息

Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw 00-662, Poland.

Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Warsaw 02-097, Poland.

出版信息

Bioinformatics. 2022 Dec 13;38(24):5440-5442. doi: 10.1093/bioinformatics/btac709.

DOI:10.1093/bioinformatics/btac709

PMID:36315072

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9750118/

Abstract

SUMMARY

The detection of the structural variants (SVs) using Illumina sequencing of human DNA is not an easy task. Multiple approaches have been proposed; however, all the methods have their limitations. In this article, we present ConsensuSV pipeline that aids the research in complex variant detection. By using consensus meta-approach, eight independent SV callers are being used to identify a uniform set of high-quality SVs. The pipeline works using raw sequencing data and performs all the necessary steps automatically, significantly reducing the researchers' time required for processing the data. The output files contain SVs, single nucleotide polymorphisms and Indels. The pipeline uses luigi framework, allowing the software to be run efficiently and parallelly using the high-performance computing infrastructure. We strongly believe that the software is useful to the scientific community interested in the germline variant detection.

AVAILABILITY AND IMPLEMENTATION

https://github.com/SFGLab/ConsensuSV-pipeline.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

摘要

使用人类 DNA 的 Illumina 测序来检测结构变异（SV）并非易事。已经提出了多种方法；然而，所有方法都有其局限性。在本文中，我们提出了 ConsensuSV 管道，该管道有助于复杂变体检测的研究。通过使用共识元方法，使用八个独立的 SV 调用者来识别一组统一的高质量 SV。该管道使用原始测序数据工作，并自动执行所有必要的步骤，大大减少了研究人员处理数据所需的时间。输出文件包含 SV、单核苷酸多态性和 Indels。该管道使用 luigi 框架，允许使用高性能计算基础设施有效地并行运行软件。我们坚信，对于有兴趣进行种系变异检测的科学界来说，该软件是有用的。