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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.
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Submitted on : Tuesday, June 23, 2020 - 2:28:08 PM
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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⟩



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