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
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