On Sun, Jan 13, 2013 at 05:05:55PM -0500, Adrian Pelin wrote: > Well, this just goes to show me how important it is to always know what > you are talking about. My apologies. I have been introduced to Ray about > 2 years ago and thought I remembered somewhere SOAPdenovo mentioned. Now > I see that it was actually OpenAssembler that was been mentioned. > > Anyway, I was wondering if I could have some advice on a dataset I am > working on. So here is some info: > - We sequenced an organism that has an estimated genome size of 6 to 12 MB. > - The technology was illumina, MiSeq 250 bp x 2 Paired End with a > fragment/insert of 500. > - The DNA quality was not super, so the fragment size ended up being 300 > actually, and our 250 x 2 reads overlap a lot. > - The nucleotide coverage of some already assembled contigs is 150 - 300 > area. > > I have already tried an assembly with Ray. I have used kmer 213, but
That is very high. > used the -short option as opposed to shortpaired. Ray does not have a -short option, I am not sure I understand what you mean. > Contigs >= 500 nt > Number: 14844 > Total length: 18556037 > Average: 1250 > N50: 1372 > Median: 914 > Largest: 61137 > > Any advice? I tried trimming reads to 50bp from 3' end and assembling, > and ray didn't like that. I got the largest scaffold 7kb. Kmer 45. Can you provide your command line ? > Adrian > > > > On 1/13/2013 4:24 PM, Sébastien Boisvert wrote:cat > > On Sun, Jan 13, 2013 at 12:17:21PM -0500, Adrian Pelin wrote: > >> Hello, > >> > >> I would like to know, since Ray is based on SOAPdenovo to my > >> understanding, > > Ray is not based on SOAPdenovo. > > > >> is there a version of Ray that is upcoming that will be > >> based on SOAPdenovo2? > > Well no since Ray has never been based on SOAPdenovo or anything else. > > > >> Adrian > >> > >> ------------------------------------------------------------------------------ > >> _______________________________________________ > >> Denovoassembler-users mailing list > >> [email protected] > >> https://lists.sourceforge.net/lists/listinfo/denovoassembler-users > ------------------------------------------------------------------------------ Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122412 _______________________________________________ Denovoassembler-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
