MUM&Co：通过全基因组比对准确检测所有 SV 类型。

MUM&Co: accurate detection of all SV types through whole-genome alignment.

机构信息

Laboratory of Computational and Quantitative Biology, CNRS, Institut de Biologie Paris-Seine, Sorbonne Université, Paris F-75005, France.

出版信息

Bioinformatics. 2020 May 1;36(10):3242-3243. doi: 10.1093/bioinformatics/btaa115.

DOI:10.1093/bioinformatics/btaa115

PMID:32096823

Abstract

SUMMARY

MUM&Co is a single bash script to detect structural variations (SVs) utilizing whole-genome alignment (WGA). Using MUMmer's nucmer alignment, MUM&Co can detect insertions, deletions, tandem duplications, inversions and translocations greater than 50 bp. Its versatility depends upon the WGA and therefore benefits from contiguous de-novo assemblies generated by third generation sequencing technologies. Benchmarked against five WGA SV-calling tools, MUM&Co outperforms all tools on simulated SVs in yeast, plant and human genomes and performs similarly in two real human datasets. Additionally, MUM&Co is particularly unique in its ability to find inversions in both simulated and real datasets. Lastly, MUM&Co's primary output is an intuitive tabulated file containing a list of SVs with only necessary genomic details.

AVAILABILITY AND IMPLEMENTATION

https://github.com/SAMtoBAM/MUMandCo.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

摘要

MUM&Co 是一个单一的 Bash 脚本，利用全基因组比对 (WGA) 来检测结构变异 (SV)。使用 MUMmer 的 nucmer 比对，MUM&Co 可以检测大于 50bp 的插入、缺失、串联重复、倒位和易位。它的多功能性取决于 WGA，因此受益于第三代测序技术生成的连续从头组装。与五个 WGA SV 调用工具进行基准测试，MUM&Co 在酵母、植物和人类基因组中的模拟 SV 上优于所有工具，在两个真实的人类数据集上表现相似。此外，MUM&Co 特别独特的是，它能够在模拟和真实数据集找到倒位。最后，MUM&Co 的主要输出是一个直观的制表文件，其中包含一个 SV 列表，只包含必要的基因组细节。