> ________________________________________ > De : Marco van het Hoog [ma...@vanhethoog.com] > Date d'envoi : 20 janvier 2015 19:50 > À : Sébastien Boisvert > Objet : Ray assembly of Hamster genome. > Hello Sébastien ...
Hi, > I am working for the National Research Council, Biotechnology Research > Institute in Montreal, and therefore (like you) I have access to all the > Calcul Quebec servers, including Colosse and Guillimin. I don't have to these resources now because I am currently working in the U.S. > We just received 3 HiSeq lanes of reads to construct a genome assembly > of a Hamster CHO cell line. > The estimated genome size of Hamster is about 2.8 GB, for Human (if I > remember well) it's about 3.3 GB, so it's a similar size. > The 3 lane coverage should be around 30X. > Could you tell me, if you were to start such a project with Ray, what > kind of settings you would use? Take a look at the Ray job scripts that were used for the Assemblathon 2: https://github.com/sebhtml/assemblathon-2-ray > Would you use Colosse and Guillimin with 30 cores each, or would you use > Mammouth Parallèle with 256 or 512 GB in memory? You would want to use many machines with something like 24 GB RAM each. > The memory requirements of Ray are a bit confusing to me :) > Thanks in advance for any suggestion. > - Marco. > ------------------------------------------------------------------------------ Dive into the World of Parallel Programming. The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
