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

TitleMUM&Co: Accurate detection of all SV types through whole genome alignment
Publication TypeJournal Article
Year of Publication2020
AuthorsO'Donnell, S, Fischer, G
JournalBioinformatics (Oxford, England)
Paginationbtaa115
Date Published2020/02/25
ISBN Number1367-4811
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 50bp. Its versatility depends upon the WGA and therefore benefits from contiguous de-novo assemblies generated by 3rd generation sequencing technologies. Benchmarked against 5 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: https://github.com/SAMtoBAM/MUMandCo. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

URLhttps://pubmed.ncbi.nlm.nih.gov/32096823
Short TitleBioinformatics

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