[mira_talk] Re: Assembling "contigs" from previous assemblies (Was Re: debris file and lrc)

On Thursday 19 February 2009 mark.rose@xxxxxxxxxxxx wrote:
> Let me explain more clearly what my situation is and goals are.  

Having  had the week-end to think this thing through: what you have there 
seems more like a finishing problem to me than an assembly problem. And here 
I'll follow Sven: you really might want to try dedicated finishing programs for 
that like, e.g., gap4. For these kind of things there is, unfortunately, no 
magic bullet.

If your contigs contain paired-end reads, it might be a good idea to see 
whether a scaffolding tool (Bambus? Others?) can help by rounding up your data 
into larger scaffold before going into finishing.

> Just wondering too, given my limited goals for these assemblies, whether
> a tool like velvet might be an alternative?

My experience with velvet is rather limited, so I cannot give advice there.

In general, I have to feeling that your assembly is not a simple bacterium but 
rather a eukaryote of medium to high complexity (with a corresponding high 
number of contigs after assembly), which makes manual finishing a rather 
tedious thing to do. I therefore can understand that you want to try if 
assemblers can do that. In that case, you probably need to "dumb them down" to 
simple alignment programs as some of them do make assumptions that are not 
valid for your scenario.

One last thing for this mail: depending on the repetitive complexity of your 
genome and which assembler you used to generate the contigs with which you're 
working with, you should take into account that reads of some repeats end up 
unassembled. Therefore you might want to see whether you can use those 
unassembled reads to build simple contigs that could close one or another hole 
in your data.

Regards,
  Bastien


-- 
You have received this mail because you are subscribed to the mira_talk mailing 
list. For information on how to subscribe or unsubscribe, please visit 
http://www.chevreux.org/mira_mailinglists.html

Other related posts: