Hi, nikos ioannidis a écrit : > Hello, > > i want to ask is there any way to compute the best K-mer to use in > order to get the best results?
I don't think so. Longer k-mers provides more specificity but also decreases usable coverage. > Also how can i measure the memory consumption? When running Ray, there are lines that contains "assembler memory usage". Like this: Rank 25 reached 16800 vertices from seed 0, flow 1 Speed RAY_SLAVE_MODE_EXTENSION 6094 units/second Rank 25: assembler memory usage: 71636 KiB Rank 25 reached 16900 vertices from seed 0, flow 1 Speed RAY_SLAVE_MODE_EXTENSION 6094 units/second Rank 25: assembler memory usage: 71636 KiB Rank 25 reached 17000 vertices from seed 0, flow 1 Speed RAY_SLAVE_MODE_EXTENSION 6191 units/second Rank 25: assembler memory usage: 71636 KiB Rank 25 reached 17100 vertices from seed 0, flow 1 Speed RAY_SLAVE_MODE_EXTENSION 6347 units/second Rank 25: assembler memory usage: 71636 KiB Rank 25 reached 17200 vertices from seed 0, flow 1 Speed RAY_SLAVE_MODE_EXTENSION 5796 units/second Rank 25: assembler memory usage: 71636 KiB Each MPI rank use memory. > And i can't find how i can measure the error corretion that the > algorithm does? Ray does not perform error correction. Instead, it just avoids erroneous k-mers. > ( actually ray does error correction or tries to resolve this using > different libraries?) Different paired libraries are indeed used to compute contig paths from the distributed de Bruijn graph. > is there any site providing different libraries inputs from different > genomes(currently i'm testing with the data from the GAGE > http://gage.cbcb.umd.edu/index.html)? You can obtain data from the sequence read archive. (ENA in Europe). > > Thank you, > Nikos > > sorry if the questions are too many. ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Denovoassembler-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
