[Bioc-sig-seq] packages for sequence assembly?

[Dan Bolser]

Sorry ... GMail just gave me a 'server error 700' I'll try resending
this at the risk of creating duplicates...

On this topic...

I heard about R analysis for recalling the encoded Solexa image files
(are these the Bustard files?). Is such a sophisticated base calling
analysis also available for SFF files for the Roche 454 data?

The 454 error model (tendency for poly-nucleotide repeats) seems
suitable for capturing in a HMM... is there facility in R to build HMM
based read mapping?

I think it could be very interesting to try to develop this.

Cheers,
Dan.


2009/7/15 Sean Davis <seandavi at gmail.com>:
> On Wed, Jul 15, 2009 at 12:21 AM, Purnachander <purna at atc.tcs.com> wrote:
>
>> Dear R-users,
>>
>> I'm working on assembly of DNA fragments. I'd like to know which "R
>> packages" contribute towards assembly of fragments being sequenced.
>>
>
> Hi, Purna.
>
> I don't think there are any specifically for that purpose.  You might want
> to look here for a relatively complete list of other software that might
> suit your needs:
>
> http://seqanswers.com/forums/showthread.php?t=43
>
> Sean
>
>        [[alternative HTML version deleted]]
>
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