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

O'Donnell, Fischer (2020) MUM&Co: accurate detection of all SV types through whole-genome alignment Bioinformatics (IF: 5.8) 36(10) 3242-3243

Abstract

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.https://github.com/SAMtoBAM/MUMandCo.Supplementary data are available at Bioinformatics online.© The Author(s) 2020. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Links

http://www.ncbi.nlm.nih.gov/pubmed/32096823
http://dx.doi.org/10.1093/bioinformatics/btaa115

Similar articles

Tools