Actually we tried multiple wet lab appraoches on known samples, at the same time. I have targeted (liquid pull down) capture of the whole region plus other haplotypes I have key PCR regions done on illumina, 454, pacbio CCS I have long reads pacbio
I'm fiddling with all of these to test haplotype resolution vs cost. I really think colored graphs are the best/fastest approach to the problem, but resolving the small details (getting high resolution) is more problematic. assemblers tend, by design, to pick one path in a bubble and ignore the other. In my case the best resolution information IS the bubble (unless it's an error). Louis On 14-09-03 11:39 AM, Adrian Pelin wrote: > What sort of NGS did you use? How long are the reads? > > Sincerely, > Adrian > > On Sep 3, 2014, at 11:32 AM, "Boisvert, Sebastien" <boisv...@anl.gov> wrote: > >>> ________________________________________ >>> 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 >>> ------------------------------------------------------------------------------ >>> Slashdot TV. >>> Video for Nerds. Stuff that matters. >>> http://tv.slashdot.org/ >>> _______________________________________________ >>> Denovoassembler-users mailing list >>> Denovoassembler-users@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/denovoassembler-users >> >> ------------------------------------------------------------------------------ >> Slashdot TV. >> Video for Nerds. Stuff that matters. >> http://tv.slashdot.org/ >> _______________________________________________ >> Denovoassembler-users mailing list >> Denovoassembler-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/denovoassembler-users ------------------------------------------------------------------------------ Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
