Question: Comparing Multiple Genome Assemblies With Reference
0
gravatar for Abhi
7.5 years ago by
Abhi1.5k
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.

-Abhi

assembly • 2.5k views
ADD COMMENTlink written 7.5 years ago by Abhi1.5k
3
gravatar for Louis Letourneau
7.5 years ago by
Montreal
Louis Letourneau790 wrote:

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/

ADD COMMENTlink written 7.5 years ago by Louis Letourneau790

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

ADD REPLYlink written 7.5 years ago by Abhi1.5k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1305 users visited in the last hour