Question: 454 And Opgen Assembly
2
gravatar for Lee Katz
7.7 years ago by
Lee Katz2.9k
Atlanta, GA
Lee Katz2.9k wrote:

What is everyone's opinion about Opgen? I believe their mapping software is called Opgen. I have been asked to use Opgen data with 454 and am wondering what everyone's experience is before I go using it.

  • How does Opgen data look?
  • How do MapIt results turn out? Is it good software?
  • Has anyone combined Opgen with an assembly or especially 454 data? How?

Thank you.

assembly • 1.6k views
ADD COMMENTlink written 7.7 years ago by Lee Katz2.9k

This also seems to be a new technology so I think very few people have had experience with it, even fewer had experience with both 454 and Opgen. Interesting question though as I haven't heard of this technology before.

ADD REPLYlink written 7.7 years ago by Istvan Albert ♦♦ 77k
3
gravatar for Louis Letourneau
7.7 years ago by
Montreal
Louis Letourneau790 wrote:

We've used their optical maps to assemble a bacterial genome.

One you've chosen the right enzyme, it's a really good tool to validate a genome!

Even with paired reads we found inverted contigs when compared to the map. These were 'easily' solved with sanger reads. We had to do another round of pairs later, this solved it also.

It's also a usefull tool to compare assemblers. We compared newbler with wgs-assembler (celera/cabog) with this.

For genomes >2Mb, you'll probably need multiple maps and you'll need to assemble these maps...that gets complicated.

ADD COMMENTlink written 7.7 years ago by Louis Letourneau790
2
gravatar for Kasycas
7.7 years ago by
Kasycas20
Dublin, Ireland
Kasycas20 wrote:

Hi,

I've used optical maps in order to look at assembled 454 contigs and it has worked brilliantly. You can see how much of your genome is covered by your assembly and where (and how big) the gaps are.

Opgen data is simple and you can get 2 outputs. One is hierarchical tree based on the similarity between whatever number of genomes you send in (and any others in their database I think). This gives you a quick indication of the similarity between genomes. The second output is the optical map which is simply a rectangular box split up by vertical lines wherever the restriction enzyme occurs in the sequence.

Once you have your contigs, Opgen software will in silico digest them and place them onto the optical map where the patterns match. Sometimes your contigs will be too small for this and this is an issue with sequencing and the assembly process. From my own experience with a 4.5Mb genome, it is a good tool to use as opposed to mate pair genome sequencing for orientating contigs and getting a idea of how much sequence you are missing etc.

Good luck!

ADD COMMENTlink written 7.7 years ago by Kasycas20
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