The coverage distribution contains, for each coverage value, the number of k-mers with such a coverage.
The library statistics estimate the fragment lengths for your libraries. See MANUAL_PAGE.txt For the "optimizations", shorter k-mers are less specific. Using longer k-mers will produce longer sequences provided that you have plenty of coverage to survive the sequencing errors. Le 2012-05-01 00:42, Habib R a écrit : > Hi Sebastien, > > How do you interpret CovergaeDistribution analysis and LibraryStats? I want > to optimize the k-mer value to get better contigs/scaffolds. Or, do you > have a script to do such optimization.... > > > *Habib Rijzaani* > > BB-Biogen, Badan Litbang Pertanian, Kementerian Pertanian > Jl. Tentara Pelajar 3A > Bogor 16111 > +62 251 8337975 > > > On Mon, Apr 30, 2012 at 11:02 PM, Sébastien Boisvert< > [email protected] >> wrote: >> Le 2012-04-30 01:30, habibr a écrit : >>> if there is no annotation file, no processing or loading annotation >> required, isn't it? >> >> Indeed, only sequence reads are required for de novo assemblies. >> >> >> >>> --- >>> Reply to this email directly or view it on GitHub: >>> >> https://github.com/sebhtml/ray/commit/dc6a063e88f24865a4af12ea46778ed2709cd251#commitcomment-1272738 >> >> --- >> Reply to this email directly or view it on GitHub: >> >> https://github.com/sebhtml/ray/commit/dc6a063e88f24865a4af12ea46778ed2709cd251#commitcomment-1274339 >> > --- > Reply to this email directly or view it on GitHub: > https://github.com/sebhtml/ray/commit/dc6a063e88f24865a4af12ea46778ed2709cd251#commitcomment-1277046 ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Denovoassembler-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
