> Allowing ray to automatically set -minimumCoverage and -peakCoverage the > estimated coverage and genome length is completely wrong
Why is that so ? > I'm interested in knowing how ray uses such parameters: it simply deletes all > nodes in the k-mer graph that are composed by kmers that appear more than > peakCoverage or it does some more sophisticated? In short, it does some more sophisticated things. Go read our publications to learn how Ray works. http://denovoassembler.sourceforge.net/publications.html You can also read files from the directory Documentation/ https://github.com/sebhtml/ray/tree/master/Documentation > Moreover, how -repeatCoverage affects the assembler performances and the > final result? In my opinion, these parameters should remained untouched. Ray does a great job at finding these values if your data has redundant k-mers. > ________________________________________ > De : Francesco Vezzi [[email protected]] > Date d'envoi : 31 août 2011 04:40 > À : [email protected] > Objet : [Denovoassembler-users] Peak coverage option > > Dear Ray users and developers, > I'm using Ray in order to assemble an highly repetitive plant genome using > Illumina and 454 reads. It is well known that the genome is composed of long > stretches of microsatellites. > Allowing ray to automatically set -minimumCoverage and -peakCoverage the > estimated coverage and genome length is completely wrong. I'm interested in > knowing how ray uses such parameters: it simply deletes all nodes in the > k-mer graph that are composed by kmers that appear more than peakCoverage or > it does some more sophisticated? > > Moreover, how -repeatCoverage affects the assembler performances and the > final result? > > Thanks > Francesco > > -- > > Francesco Vezzi, PhD Student > Tel: +39 3805151541 > Department of Mathematics and Computer Science, > University of Udine, Udine, Italy > & > Applied Genomics Institute (IGA), Udine, Italy > http://www.appliedgenomics.org > > > > ------------------------------------------------------------------------------ Special Offer -- Download ArcSight Logger for FREE! Finally, a world-class log management solution at an even better price-free! And you'll get a free "Love Thy Logs" t-shirt when you download Logger. Secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsisghtdev2dev _______________________________________________ Denovoassembler-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
