That sounds like a good idea.
I am in the process of preparing my thesis defense / relocating for a postdoctorate and therefore I am quite occupied. I can review code on denovoassembler-devel. On 21 mars 2014 17:43, David Eccles (gringer) [bioinformat...@gringene.org] wrote: > À : denovoassembler-users@lists.sourceforge.net > Objet : [Denovoassembler-users] Digital Normalisation > > Is there any chance of implementing digital normalisation natively in Ray? > I'm currently using Trinity's paired-end normalisation procedure, > but I expect it would be much slower than what Ray would be able to achieve > with a native version: > > http://trinityrnaseq.sourceforge.net/trinity_insilico_normalization.html > http://ivory.idyll.org/blog/what-is-diginorm.html > > The general process is to look at the distribution of counts of kmers in each > sequence to get an idea of coverage, then decide on whether to > include or discard a read based on that count distribution together with a > target coverage. If assemblies work better at 100X coverage than > 500X coverage (or there is no substantial benefit from higher coverage), then > it makes sense to discard reads when you can be pretty > confident that you've already reached 100X coverage for all (or most) kmers > in that read. > > - David > > ------------------------------------------------------------------------------ > Learn Graph Databases - Download FREE O'Reilly Book > "Graph Databases" is the definitive new guide to graph databases and their > applications. Written by three acclaimed leaders in the field, > this first edition is now available. Download your free book today! > http://p.sf.net/sfu/13534_NeoTech > _______________________________________________ > Denovoassembler-users mailing list > Denovoassembler-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/denovoassembler-users ------------------------------------------------------------------------------ Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
