[mira_talk] Re: Solexa Assembly
- From: Lionel Guy <guy.lionel@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 17 Jan 2011 17:13:55 +0100
Think that 2x100bp solexa reads with 200bp insert size are in total 400bp,
shorter than the median size of 454 Titanium reads. Any repeat longer than that
won't be further solved.
If you want to assemble further, sequence a mate-pair library with longer
insert size, preferably several (e.g. 3, 8, 12, 20 kb). I can't see any way of
closing further gaps by bioinformatics means only.
On 17 Jan 2011, at 16:23 , Sandrine Moreira wrote:
> Hi,
>
> I'm suprised by the answer of Bastien, don't you think that the solexa reads
> will help to fill the gaps ?
>
> So, what would be the better strategy in the case of Aayushmaan: re-building
> a new assembly from scratch with both set of sequences or, as Aayushmaan
> propose, considering the 454 scaffolds as reads and doing a denovo(-like ! )
> assembly with the new Solexa reads ?
>
> SaM
>
> Le 2011-01-15 à 7:38 AM, Bastien Chevreux a écrit :
>
>> On Jan 14, 2011, at 8:34 , Aayushmaan/Scube wrote:
>>> Thanks for your reply & info. I killed this run. I have 454 data of the same
>>> genome and used celera for assembling it & got 29 scaffolds. If I run a
>>> hybrid denovo using these 29 scaffolds & the 200bp solexa library will mira
>>> be able to give better results?
>>
>> You mean taking the 29 scaffold sequences and treat the as reads? That will
>> be possible only for scaffolds <20kb, which I expect will not be the case
>> for most of your scaffolds.
>>
>> Then again: what does "better" mean for you? If you expect longer
>> contigs/scaffolds, that is improbable. If you want to get rid of the pesky
>> consensus errors of the 454 data, that is very probable.
>>
>> B.
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