[mira_talk] Re: Megahub info

Hi Bastien!
I am not quite sure what teh combined mapping and de-novo assebly is; would 
this actually join the reference contigs? If so I should go back and read the 
manual better..

A mapping assembly could be ok for now, but in principle I am against this 
approach;
In our genome projects we might have in the range of 10-100 shotguned PCR 
products (for eukaryotes I guess it might be much much more). Doing a mapping 
(as far as i understand) will break the assembly at all these sites, and they 
will then have to be manually joined, which is prone to human errors, and lacks 
all the nice features that the assembler has (detecting ambiguities, properly 
handle paired-end info etc.). The gloomy result might therefore be that you 
spend much time making your PCR:s assemblies  and then fail to properly join 
your contigs in the end anyway. 

I think that a proper handling of really long sequences would be great in the 
gap-closure phase of a genome project. (This is also the only area where phrap 
is still beating MIRA...)

B




On Thu, 25 Jun 2009 19:43:23 +0200
Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:

> On Donnerstag 25 Juni 2009 Björn Nystedt wrote:
> > [...]
> > I think the megahub is actually an artefact; the single read in the megahub
> > logfile is a long (15kb) fake read comprising a complete PCR product. (The
> > complte run is 300000 GS20, 16000 Sanger and ~20 PCR fake reads)
> 
> Ah ... the fake PCRs is some crucial info which was missing. Yes, that 
> explains a bit the behaviour.
> 
> You sure you don't want to do a mapping assembly? Or a combined mapping and 
> de-novo assembly?
> 
> Regards,
>   Bastien
> 
> 
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Björn Nystedt (Sällström)
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Molecular Evolution
EBC, Uppsala University
Norbyv. 18C, 752 36  Uppsala
Sweden
phone: +46 (0)18-471 45 88
email: Bjorn.Nystedt@xxxxxxxxx
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