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

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.