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Old 09-05-2015, 12:48 AM   #19
suzumar
Junior Member
 
Location: France

Join Date: Sep 2012
Posts: 2
Default Coverage Binning

Hi Brian
I am trying to assemble a genome from single cell amplification using spades and subsequently using tetramer + coverage analysis (i.e. CONCOCT) to remove "contaminating reads" which seem to be created at the sequencing. If I understood correctly bbnorm will keep enough information to allow coverage information to be used subsequently to bin contigs. Is that the case?

I also would like to know your opinion on how bbnorm compares to the strategy described in http://www.sciencemag.org/cgi/conten.../6047/1296/DC1

I quote:

"High-depth k-mers,presumably derived from MDA amplification bias, cause problems in the assembly, especially if the k-mer depth varies in orders of magnitude for different regions of the genome. We removed reads representing high-abundance k-mers (>64x k-mer depth) and
trimmed reads that contain unique k-mers. The results of the k-mer based coverage normalization are shown in table S8."
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