Hi, [I CC'ed the mailing list as this is Ray-related.]
On 12/03/2012 11:33 AM, Forster, Robert wrote: > Hi Sebastien: > > I’ve been investigating using Ray for my metagenomic samples (discussed this > on the list a few months ago). I’ve used Ray rc 2.08 You mean Ray 2.0.0-rc8 ? >on four samples of HiSeq data(one lane each sample/treatment) and I end up >reducing the dataset, but still have 3.5 million or >so contigs in each sample (N50 143,contigs > 500 89,700 N50 1137, largest >37kb). What k-mer length are you using ? How many reads per sample do you have ? Did you run Ray with paired reads ? > I am in the stages of convincing my Centre to >purchase a MiSeq, so I can get 2x250 reads as well, hoping this will help. How are you preparing your DNA libraries ? What's the insert size ? With de Bruijn graph assemblers, what's important to get through repeats is mostly good insert sizes. > If not, I will contract this out in January. I do have >some single read 454 data as well. > > The experiment is a unique one, using the rumen of MuskOxen fed straw to look > for biomass degrading enzymes. We published a >metatranscriptome paper in PLoS One about the rumen fungal enzymes, but I’d >like to get a better handle on the metagenome >sequencing I’ve done. > Sure. > I found a talk on-line that you did at Argonne about metagenome assembly. So > I’m curious about Ray Meta. Is it possible >to test it out as compared to the standard Ray? > Ray Meta is a workflow with Ray. The heuristics of Ray 2.0.0-rc8 are those of Ray Meta. Our paper describing Ray Meta was accepted for publication in the journal Genome Biology. It should appear soon on the publisher website. > Also, once I get new the MiSeq reads (another possible 15 GB per sample) the > assembly may be beyond our capacity here >in Lethbridge. I was wondering whether you may be interested in a >collaboration to analyse the data? Yes. That would be interesting. > > Bob > > Robert J. Forster, Ph.D. > Rumen Microbial Ecology/Genomics > Lethbridge Research Centre > Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada > 5403 1st Ave. S. > Lethbridge, AB T1J 4B1 > robert.fors...@agr.gc.ca <mailto:robert.fors...@agr.gc.ca> > Telephone | Téléphone 403-317-2292 > Facsimile | Télécopieur 403-382-3156 > > Government of Canada | Gouvernement du Canada > ------------------------------------------------------------------------------ Keep yourself connected to Go Parallel: BUILD Helping you discover the best ways to construct your parallel projects. http://goparallel.sourceforge.net _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
