Skip to Main content Skip to Navigation
Journal articles

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

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.
Document type :
Journal articles
Complete list of metadatas

Cited literature [8 references]  Display  Hide  Download

https://hal.sorbonne-universite.fr/hal-02879014
Contributor : Hal Sorbonne Université Gestionnaire <>
Submitted on : Tuesday, June 23, 2020 - 2:28:08 PM
Last modification on : Monday, August 31, 2020 - 12:30:19 PM

Files

 Restricted access
To satisfy the distribution rights of the publisher, the document is embargoed until : 2020-12-23

Please log in to resquest access to the document

Identifiers

Citation

Samuel O'Donnell, Gilles Fischer. MUM&Co: accurate detection of all SV types through whole-genome alignment. Bioinformatics, Oxford University Press (OUP), 2020, 36 (10), ⟨10.1093/bioinformatics/btaa115⟩. ⟨hal-02879014⟩

Share

Metrics

Record views

16