> ________________________________________
> From: Louis Letourneau [louis.letourn...@mail.mcgill.ca]
> Sent: Tuesday, August 26, 2014 8:52 AM
> To: denovoassembler-us...@lists.sf.net
> Subject: [Denovoassembler-users] Ray for HLA analysis
> I was wondering if someone would have ideas/insight on how to apply Ray
> (colored debruijn graph) to HLA analysis.
> Bit of background (skip this if you want to skip to the Ray part):
> --->
> HLA are genes is a region of the human genome (MHC region) that is highly
> polymorphic. There are 2 classes of genes in the MHC region.
> Genes that are interesting are usually HLA-A, HLA-B, HLA-D*
> These are important for individual typing for organ donations, skin graph,
> etc, etc.
> There are over 12,000 differently known/reported alleles (between genes) in
> this region.
> There are typically 2 techniques to target this region, either target some
> key regions (incomplete but good enough), or sequence the whole thing.
> --->
> There many tools that kind of do this, but they all have problems.
> I am trying Ray communities and Ray surveyor for this but I'm wondering which
> would be better suited (before I get my results) for this task
> Communities using the known alleles as a reference set
> or
> Surveyor using kmers built for each alleles as reference set.
> (also is there a way to get ray to just build the kmers.txt file without
> doing the rest?)
-graph-only
Exits after building graph.
> What are your thoughts, if thoughts you have :-)
> Thanks
> Louis
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