> From: Adrian Pelin [apeli...@gmail.com] > Sent: Sunday, May 18, 2014 6:59 PM > To: Denovoassembler-users@lists.sourceforge.net > Subject: Re: [Denovoassembler-users] Assembling polyploid genomes > > > > Hello, > > I am working with a tetraploid dataset, and most assemblies generate > redundancy (small contigs representing different haplotypes of a small region > belonging to a different contig). > > > This provides me with an assembly that is neither haploid nor diploid nor > tetraploid. Is there any way to remove these redundant contigs or assemble in > such a way as to not create them? My homozygous nucleotide coverage is about > 120x, and the dataset is HiSeq > 100x2 bp.
The short seeds you are getting are presumably caused by using a k-mer length such as ( 2 * k ) > 100 nucleotides. There is an option called -merge-seeds which merges seeds initially to reduce running time. But this option is not totally stable yet. You are free to try it. > > Thank you, > Adrian > > ------------------------------------------------------------------------------ "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE Instantly run your Selenium tests across 300+ browser/OS combos. Get unparalleled scalability from the best Selenium testing platform available Simple to use. Nothing to install. Get started now for free." http://p.sf.net/sfu/SauceLabs _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
