Maybe both are correct as well.
At this point, you can take scaffolds and validate contig order against the reference. I wrote a tool for that that utilisez MUMmer. MUMmer is an aligner for large sequences and was co-published by the researchers that did the GAGE thing. The tool is available on my github in the Ray-TestSuite project. Example: ValidateGenomeAssembly.sh bacterialReference.fasta RayOutput/Contigs.fasta Ray-assembler This will do a lot of checks to assess the quality of the assembly, using the MUMmer tool as the comparison engine. nikos ioannidis a écrit : > Well, if i use a reversing algorithm and reverse the short jumps > from this : > <-------------- ---------------> > to this : > > ------------><-------------- > i get diferrent results, for example for the Staphylococcus aureus of > GAGE site with k31 > > i get without reversing the shortjumps: > > > N50 for Contigs>= 100 nt 15862 > N50 for Contigs>= 500 nt 16024 > N50 for Scaffolds>= 100 nt108215 > N50 for Scaffolds>= 100 nt 108215 > > > > and with reversing the shortjumps: > > > N50 for Contigs>= 100 nt 15862 > N50 for Contigs>= 500 nt 15862 > N50 for Scaffolds>= 100 nt 168850 > N50 for Scaffolds>= 100 nt 168850 > > and for k21 > > i get without reversing the shortjumps: > > > N50 for Contigs>= 100 nt 30722 > N50 for Contigs>= 500 nt 30722 > N50 for Scaffolds>= 100 nt161951 > N50 for Scaffolds>= 100 nt 161951 > > > and with reversing the shortjumps: > > > N50 for Contigs>= 100 nt 31077 > N50 for Contigs>= 500 nt 31637 > N50 for Scaffolds>= 100 nt 222525 > N50 for Scaffolds>= 100 nt 222525 > > > The main diferrence is at the scaffolds, is it normal ? what results > are for you seems correct? > > > Thank you > > > > > On Mon, May 28, 2012 at 7:32 PM, nikos ioannidis<niioa...@gmail.com> wrote: >> Sorry I have made a mistake, >> in the previous post I was talking about Short jump libraries, >> so is there anything i need to do in order to insert these reads in the Ray? >> Because for example in Velvet i think the user have to reverse the library >> with some tool before, >> while in ALLPATHSLG that is not nesessary. >> >> Also about Long jump libraries the same question. >> >> >> Thank you and sorry for the previous post. > ------------------------------------------------------------------------------ > 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 > Denovoassembler-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/denovoassembler-users ------------------------------------------------------------------------------ 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 Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
