On 20/03/13 09:44 PM, Adrian Pelin wrote: > Salut Sebastien, > > Is the plugin ready? Is it integrated in the Ray assembly or used on > .fasta contigs after assembly is done? I noticed the files for it have > been uploaded. >
It about 70% done. Around 8-15 hours left to put on it. Should be done this week. > Adrian > > On 3/18/2013 5:15 PM, Sébastien Boisvert wrote: >> Hi, >> >> On 18/03/13 12:20 PM, Adrian Pelin wrote: >>> Hello, >>> >>> It seems like the answer I got from the velvet mailing list for this issue >>> is that there is no solution. >>> Is there a strategy I could use use with Ray to avoid getting the following >>> issue?: >>> >>> My organism seems to be full of SNPs in a perfect 50/50 ratio which is >>> probably due to it being diploid. My expirience with assembling velvet >>> data is that it generates multiple contigs with very high nucleotide >>> identity between some contigs. The only diffrences are SNPs. >>> >>> I was wondering, is there any way to assemble only the haploid genome >>> for a start? I am afraid to overestimate the haploid genome size. Also, >>> velvet doesn't generate identical contigs for each piece of sequence, >>> just in some cases there are giant contigs over a few kb overlapping. >>> >>> Any strategy to avoid this or remove these from assembly? My data is >>> MiSeq fragments 300bp and hiseq mate pair jumping lib 3kb. >>> >> I happen to be working on exactly this problem in Ray today >> (I have been working on that for a few weeks now). >> >> >> See these two tickets: >> >> * https://github.com/sebhtml/ray/issues/136 >> >> * https://github.com/sebhtml/ray/issues/153 >> >> >> The thing is that in a de Bruijn graph (such as the one in Velvet or Ray), a >> variation of one nucleotide >> leads to alternate branches containing k vertices. >> >> >> A typical SNP in a de Bruijn graph (in Ray Cloud Browser): >> >> => >> http://genome.ulaval.ca:10111/client/?map=0§ion=0®ion=1&location=132207&zoom=1.191270483217418 >> >> >> >> From an algorithm point of view, if you use a large k-mer length, >> assemblers will spawn contigs for each >> allele because each branch will be "good enough". >> >> Therefore, some of these assembly seeds need to be filtered out. As far as I >> know, all de Bruijn assemblers have >> this problem right now with large kmers. >> >> >> >> The two issues above should be fixed this week by this new plugin in Ray: >> >> => >> https://github.com/sebhtml/ray/tree/master/code/SpuriousSeedAnnihilator >> >> As its name suggests, SpuriousSeedAnnihilator will annilihate spurious seeds >> which otherwise will lead >> to duplicated genetic regions. >> >> -Séb >> >>> Adrian >>> >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> Everyone hates slow websites. So do we. >>> Make your web apps faster with AppDynamics >>> Download AppDynamics Lite for free today: >>> http://p.sf.net/sfu/appdyn_d2d_mar >>> _______________________________________________ >>> Denovoassembler-users mailing list >>> Denovoassembler-users@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/denovoassembler-users >>> >> >> ------------------------------------------------------------------------------ >> Everyone hates slow websites. So do we. >> Make your web apps faster with AppDynamics >> Download AppDynamics Lite for free today: >> http://p.sf.net/sfu/appdyn_d2d_mar >> _______________________________________________ >> Denovoassembler-users mailing list >> Denovoassembler-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/denovoassembler-users >> > > > ------------------------------------------------------------------------------ > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_mar > _______________________________________________ > Denovoassembler-users mailing list > Denovoassembler-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/denovoassembler-users > ------------------------------------------------------------------------------ Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_mar _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
