[ensembl-dev] EnsEMBL gene build pipeline

Marc Hoeppner mphoeppner at gmail.com
Wed Feb 6 08:47:42 GMT 2013


Dear EnsEMBL team,

first of all, sorry of this has been asked before - if so, please point 
me in the right direction ;)

Anyway, my question concerns the gene build pipeline that EnsEMBL 
employs for the various genome projects. I would like to get a better 
understanding of how it works and - ideally - get it to work myself. We 
have been discussing various available tools for annotation at our 
department and currently entertain the idea of providing genome 
annotation as a service for other groups (seeing that EnsEMBL doesn't 
really have the capacity to take on all the genomes that are being 
sequenced nowadays). And for that I would very much like to use the 
EnsEMBL code base, since it seems to be the most mature and complete 
solution for this purpose.

I have been browsing through the available EnsEMBL documentation, got 
eHive to run for example, but I have not really come across a more 
in-depth description of which scripts to use, what data to provide and 
how to glue everything together.

I understand that there is a short course on this given each year as 
part of the Genome Informatics conference, but assuming I won't be able 
to make it to that, is there any document around to get me started?

Cheers,

Marc




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