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. 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
