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2.8 years ago
Hi , I want to identify genomic structural variations on prokaryotic genomes. I came across a tool Mugsy which can identify indels and genomic re-arrangements..However I have not been able to identify and interpret variations in the output (am opening the maf file in gmaj viewer). Can anyone suggest how to interpret the results. Could you also tell me whether there are any other tools for identifying variations on completely sequenced bacterial genomes (not on NGS data). Really appreciate the help
Thank you , Anwesha
I think you need to clarify a few things. Are you calling SVs using whole genome alignment (after assembly) or read alignment? This will be the main difference in analysis and tools. And if the latter what sequencing technology? And can you assemble a complete genome (then proceed with whole genome alignment)?
I am looking for SVs using whole genome alignment assembled genome. for eg SVs in the assembled genome of NZ_CP019870.1 Clostridioides difficile strain BR81 chromosome. The want to identify regions of the genome having SVs and see if there is any functional consequence of it
Ok great. Personally I have not tried mugsy before so I am not sure how to interpret the output. \ Myself I designed a tool MUM&Co which can detect the full range of SVs (that is the idea anyway) \ You can also look at Syri and/or SVIM-asm \ These three detect a wide range of SVs. Alternatively there is assemblytics and minimap2-paftools which do well looking for CNVs
All should be very quick and have a vcf output so should be easy to interpret For MUM&Co there is a simpler tsv file also in order to try make it even easier to interpret however for a bacterial genome the vcf should be fine
Hope that helps
Ohk thank you so much ...will check out the suggestions you have provided and get back
I have a query ....Will MUM&Co be helpful in identifying Structural Variations in prokaryotic genomes? I was going through the paper and it is indeed useful in identifying variations but in yeasts, plants and humans
It was specifically designed to work on Saccharomyces cerevisiae, but the principal is the same. One chromosome should just simplify the procedure in fact. \ Mauve is another tool designed for bacteria I believe (or just small genomes). You could also give that a whirl