Thanks Paul for your quick reply. No, it was not specifically in bioconductor context. Varienty of information regarding the quality control before and after alignment for ex, phred quality score sanger, illumina, solexa platform. So the theoretical foundation of quality control mentioned below (nucleotides quality by cycle, nucleotides frequency by cycle, GC content and distribution, K-mer frequency by cycle) based on which the functions of the bioconductor packages are defined and the quality control after alignment including but not limited to mapped reads, mean coverage, strand specificity, 5'/3' bias. Kind regards, ________________________________ From: Paul Geeleher <paulgeeleher@gmail.com> Cc: "bioconductor@stat.math.ethz.ch" <bioconductor@stat.math.ethz.ch> Sent: Friday, August 31, 2012 10:15 AM Subject: Re: [BioC] reviews for quality control Fastqc has a very good video tutorial that also explains quite a lot of general issues very well: (Although I'm not sure if you meant a tutorial in the context of Bioconductor specifically) Paul. > Hi, > It might be a trivial question but I just wonder if you could advise good theoretical tutorials, reviews on NGS (different platforms) quality control  like nucleotides quality by cycle, nucleotides frequency by cycle, GC content and distribution, K-mer frequency by cycle etc. I know that I could find good practical tutorials on bioconductor web site. > > Look forward to your reply, > > Carol > >        [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Paul Geeleher (PhD Student) School of Mathematics, Statistics and Applied Mathematics National University of Ireland Galway Ireland -- www.bioinformaticstutorials.com [[alternative HTML version deleted]]