MUM&Co is a simple bash script that uses Whole Genome Alignment information provided by MUMmer (v3 and v4) to detect variants.

MUM&Co is able to detect:
Deletions (novel and mobile), insertions (novel and mobile) and tandem duplications (>50bp)
Inversions and translocations (>1kb)

MUM&Co requires installation of MUMmer3 or 4.
MUM&Co will look for the MUMmer toolkit's scripts path using 'which xxxxx'.
This path can be editted directly in the script if required.

In order to help with downstream analysis:
Renaming and re-orientation of the query genome contigs to correspond to their reference counterparts
Tools such as RaGOO and Ragout can do this alongside scaffolding of contigs (this is not currently recommended for short-read based assemblies).

Options:

     -r or --reference_genome          path to reference genome
     -q or --query_genome              path to query genome
     -g or --genome_size               size of genome
     -o or --output                    output prefix

Test run script (keep order of options):

     bash mumandco_v*.sh -r ./yeast.tidy.fa -q ./yeast_tidy_DEL100.fa -g 12500000 -o DEL100_test

Output folder contains:
Folder with alignments used for SV detection
Txt file with summary of SVs detected
and a tsv file with all the detected SVs.

UPDATE:
For those using MUMmer4 you can use the MUM&Co script '..MUMmer4_multithreads.sh' that contains an option for increasing the thread use of the nucmer alignments This can only be run if MUMmer4 is being used as MUMmer3 does not offer this option
Options:

     -r or --reference_genome          path to reference genome
     -q or --query_genome              path to query genome
     -g or --genome_size               size of genome
     -o or --output                    output prefix
     -t or --threads                   thread number

Test run script (keep order of options):

     bash mumandco_v*_MUMmer4_multithreads.sh -r ./yeast.tidy.fa -q ./yeast_tidy_DEL100.fa -g 12500000 -o DEL100_test -t 2

Additionally there is an option to search for insertion and deletion events in the reference in order to label them as either mobile or novel events.
This requires BLAST and samtools installation.
In order to use this feature, edit the bash script to change 'blast_step="no"' to 'yes'

Reference:
Samuel O’Donnell, Gilles Fischer, MUM&Co: accurate detection of all SV types through whole-genome alignment, Bioinformatics, Volume 36, Issue 10, 15 May 2020, Pages 3242–3243, https://doi.org/10.1093/bioinformatics/btaa115