[Bioclusters] Parallel assembling of a shotgun genome

Charles Wust bioclusters@bioinformatics.org
Tue, 31 Aug 2004 18:16:43 -0300 (BRT)


Hello,

I am presently doing research in this field, but I do not have any working
version of a parallel fragment assembler yet.

But look for PCAP. It is made by the same author of CAP3, it should work
well on your cluster.

Charles

> Hi Octavio:
>
>    Have a look at SPS Phrap Suite at
> http://www.geospiza.com/tools/sps-phrap.htm .
>
> Joe
>
> Octavio Martínez de la Vega wrote:
>
>>Hi,
>>
>>We are a genomic research center in México and we will be initiating the
>>shotgun sequence of a large genome. Currently we do our bioinformatics
>>in a 32 processor cluster, but we assemble (for example ESTs sequences)
>>using Phrap and/or CAP3.
>>The question is,
>>Can I parallelize the assembling of a shotgun sequencing project to use
>>the power of a cluster?
>>
>>Thanks in advance,
>>
>>Octavio.
>>
>>------------------------------------
>>Octavio Martínez de la Vega
>>Profesor Titular
>>omartine@ira.cinvestav.mx
>>
>>
>
>
> --
> Joseph Landman, Ph.D
> Scalable Informatics LLC,
> email: landman@scalableinformatics.com
> web  : http://www.scalableinformatics.com
> phone: +1 734 612 4615
>
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