Question: Comparing Multiple Genome Assemblies With Reference
gravatar for Abhi
8.3 years ago by
United States
Abhi1.5k wrote:

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.


assembly • 2.8k views
ADD COMMENTlink written 8.3 years ago by Abhi1.5k
gravatar for Louis Letourneau
8.3 years ago by
Louis Letourneau800 wrote:

nucmer + show-coord from the MUMur ( 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.

ADD COMMENTlink written 8.3 years ago by Louis Letourneau800

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

ADD REPLYlink written 8.3 years ago by Abhi1.5k
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