On 18/11/13 06:16 PM, Bastien Chevreux wrote: > On 18 Nov 2013, at 19:47 , Sébastien Boisvert <[email protected]> > wrote: >> I (probably) found the issue. >> […] >> Working on a patch now.
Hi Bastien, (I CC'ed the list) Good to hear from the author of MIRA ! > > Thanks for that. > > Off-github: from all the pure nextgen (Illumina, late 454 reads) assemblers I > tried, I like Ray best so far. Good work there. It does have its fair share > of misassemblies >when I run it on my horror projects I have in the archive, but definitely less >than a couple of other assemblers I tested. Though it completely fails with >early 454 >and current gen Ion data, but then again dbg assemblers are not really made to >cope with pesky homopolymers and carry forward errors. Yes. Ray lacks some sort of bubble pass-through for these, > > I noticed Ray had also quite some trouble with the uneven coverage as > produced by Nextera kit preps, but I think this is inevitable for assemblers >which somehow try to deduce repetitiveness from (k-mer or other) coverage. > I agree the process could be refined. For uneven coverage: https://github.com/sebhtml/ray/issues/132 Last year, I started to work on an interactive visualizer to look at these sort of things. For instance, you can take a look at uneven coverage at http://genome.ulaval.ca:10208/client/?map=0§ion=0®ion=381&location=304&depth=10&zoom=0.6154458722734157 by pressing the "Graphs" button. The 2.x.x series is way better with uneven coverage and this is one of the changes we made to tackle metagenomes. see http://genomebiology.com/2012/13/12/R122 > Ray will be a good validation assembler for me … and for projects where I’ll > have to ditch MIRA due to the number of reads / size of the genome :-) > > Best, > Bastien > For mini-ranks: Basically, I have been playing around with various approaches to program scalable tools. Some of these approaches are error-prone while others are easier to master. So far, I can say that RayPlatform (some sort of framework on top of Ray) implements 3 models: - slave modes / master modes / message tags (RayPlatform Plugin API) - mini-rank runtime (compatible with RayPlatform Plugin API) - actor model (RayPlatform Actor Playground) I recently implemented a tool to compare many samples without a reference using kmers and the de Bruijn graph with this actor model. The code is much easier to read than distributed code that does not use this actor model. I believe you are located in Europe. will be presenting Ray and Ray Cloud Browser at Beatles and Bioinformatics in Liverpool, UK. on 27 November 2013. http://pathogenomics.bham.ac.uk/blog/2013/10/beatles-and-bioinformatics/ ------------------------------------------------------------------------------ Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk _______________________________________________ Denovoassembler-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
