Comparing Multiple Genome Assemblies With Reference

Question

[Abhi]

Hey Guys

We are doing muiltiple assemblies (using diff methods) for a given genome using NGS data. We have reference genome available and would like to see how our assembled contigs/scaffolds match up against each other and reference.

So besides the usual stats like N50, #contigs etc is there any tool out there which could compare the assembled contigs amongst different assemblies and see how different contigs look like between them.

-Abhi

Answer 1

[Louis Letourneau]

nucmer + show-coord from the MUMur (http://mummer.sourceforge.net/) is very useful to do this. I've used this many, many times.

Mauve also is a very good tool to show regions that overlap between the assemblies, although I have had problems with mauve with big genomes. Your mileage may vary. http://gel.ahabs.wisc.edu/mauve/

[Abhi]

I will try Muave as we needed something with visuals. Thanks! -A