SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
SOAP denovo assembly results bioinfosm Bioinformatics 9 06-13-2012 07:22 AM
Assembly files in new Assemblers Tools for NGS. aloliveira Bioinformatics 2 10-22-2010 04:27 AM
Another assembly tools: LOCAS (Has anyone tried already?) Gangcai Bioinformatics 0 01-28-2010 05:51 PM
List of Assembly and Analysis tools geschickten Bioinformatics 1 01-12-2010 05:14 AM
De-novo assembly of bacteria genomes - which tools? maasha Bioinformatics 8 08-12-2009 01:41 PM

Reply
 
Thread Tools
Old 04-24-2012, 10:25 PM   #1
strob
Member
 
Location: Belgium

Join Date: Nov 2008
Posts: 79
Default How two compare two assembly results? (not assembly tools)

Hi,

most of the time, people compare results, using the same dataset, but obtained from different tools (example: velvet vs. soapdenovo)

I have however two independent datasets (solexa data, obtained from two different 'extraction' methods), on which I performed seperately a de novo assembly. So I have two assemblies, coming from different data, but coming from the same species. Now I would like to compare both assemblies and see which assembly is the most satisfying to me. I have questions like: is there overlap? Is one completely imbedded in the other? Are they complementary? etc.

So simple: how to compare two independent de novo assemblies (same species)?

Thanks
strob is offline   Reply With Quote
Old 04-24-2012, 11:57 PM   #2
nickloman
Senior Member
 
Location: Birmingham, UK

Join Date: Jul 2009
Posts: 356
Default

I would use Mauve to do this and visualise the output. If you had any reference-grade genomes that you would expect to be similar and preserve gene order (synteny) you could also add that in to guide which assembly is likely to be more accurate.
nickloman is offline   Reply With Quote
Old 04-25-2012, 04:41 AM   #3
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543
Default

There is no easy answer - and it depends on what you are looking for.

For example, further to Nick's excellent comments, you might want to run a gene caller on both and compare the gene sets. If you are interested in particular genes, then you could just try TBLASTN or BLASTN to see if they are in both draft genomes or not.
maubp is offline   Reply With Quote
Old 04-25-2012, 05:05 AM   #4
strob
Member
 
Location: Belgium

Join Date: Nov 2008
Posts: 79
Default

I used two different methods to extract my DNA, which was than sequenced and assembled. I want now to know which method gave me the best results, by comparing the two assemblies. I want to find out if both methods give me the same data or if there is only a partial overlap.
Mauve is nice to visualize, but limiting. I would more like to get some overall statistics

Thanks already for the feedback
strob is offline   Reply With Quote
Old 04-25-2012, 05:10 AM   #5
nickloman
Senior Member
 
Location: Birmingham, UK

Join Date: Jul 2009
Posts: 356
Default

After you've generated a Mauve alignment you can use Mauve Assembly Metrics (http://code.google.com/p/ngopt/) to give you some stats, but this is designed to be used against some kind of baseline truth reference genome. But you could run it twice I guess with genome 1 as reference first time and genome 2 as reference second time in order to generate some numbers.
nickloman is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 09:37 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO