MUM&Co uses Whole Genome Alignment information provided by MUMmer (v4) to detect structural variants. Contains a VCF output file with all calls currently being imprecise Contains another output file containing the calls alongside the respective DNA impacted This new step requires samtools installation Now calls the reverse of tandem duplications, tandem contractions (>50bp)

MUM&Co is able to detect: Deletions, insertions, tandem duplications and tandem contractions (>=50bp & <=150kb) Inversions (>=1kb) and translocations (>=10kb)

Requirements:

-MUMmer4 -Samtools MUM&Co will look for the MUMmer toolkit's and samtools scripts path using 'which xxxxx'. An error warning will print and the script will stop if these paths cannot be found This path can be editted directly in the script if required. Easy conda installation: conda create -n mumandco_env bioconda::mummer4 bioconda::samtools

How to run:

mumandco.sh -r reference.fa -q query.fa -g 12500000

Required inputs:
   -r | --reference_genome		Fasta file containing an assembly
   -q | --query_genome		    Fasta file containing another assembly
   -g | --genome_size		    Rough estimation of genome size for both reference and query to determine alignment parameters

   Recommended inputs:
   -t | --threads			    Number of threads for alignment (default: 1)
   -ml | --minlen			    Minimum length of alignments in basepairs (Default: 50)

   Optional parameters:
   -p | --prefix			    Prefix for output files and name of output folder ('prefix'_output) (Default: mumandco)
   -b | --blast			        Adds the blast option to identify is insertions or deletions look repetitive or novel (takes significantly longer)
   -h | --help			        Print this help message

Output folder contains:

-Folder with alignments used for SV detection -Txt file with summary of SVs detected -TSV file with all the detected SVs -TSV file with all detected SVs plus the DNA associated with the event (all from reference except insertions) -VCF file with all calls currently being imprecise

Notes on tsv file:

The last column in the TSV file contains notes: -'complicated' : multiple calls within the same region; generally overlapping insertions and deletions -'double' : several calls at the same coordinates; generally tandem duplications or contractions with multiple copy changes -']chrX:xxxxxx]' : a VCF inspired notation for the association of the translocation fragments with the other fragments e.g. for chr1 with its right border at 250000bp assocaited with chr2 at 100000bp; the note would be as follows for chr 1: ']chr2:100000]' and for chr2 : '[chr1:250000[' As such, each translocation fragment as called as an event, is now a breakend-like call and will be duplicated if both borders are involved in translocations The later notation for the TSV file is currently being added to the alt column in the VCF for 'TRA' events. Currently it is not a called a breakend site (contains no nucleotide at edge) but can be interpreted similarly

MUMmer/nucmer version:

As of version 3 MUMmer4 is now required due to the hard wired thread option not available during alignment with MUMmer3

BLAST option:

The blast option (-b /--blast) using BLAST to search for insertion and deletion events in the reference/query in order to label them as either mobile or novel events. Takes significantly longer particularly with many variants and large genomes

Input suggestion:

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)

Citation:

Samuel O’Donnell and 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

MUMandCo

Install / Use

README