Hello, I have done some test with/without read filtering. From my experience, the assemblies were better without. Based on what I know of Ray, I think that giving it very high quality reads (instead of normal/high quality) will probably result in a small reduction of memory usage but the impact on final assembly would be minimal (Sebastien could confirm). >From my experience with Ray and denovo assembly, I can tell that every data set is different. I recommend you to make your own test or to re-sequence your sample to obtain a greater number of reads and better quality. Good luck!
Pier-Luc Le 2013-04-08 07:35, jjv5 a écrit : > Hello, > > Has anyone assessed the impact of trimming/filtering reads on assembly > outcome and performance? I would expect very high quality reads to use > less memory and complete assembly a little faster perhaps, but will it > make any impact on the final assembly? > > We have run some control with no filtering and the results look great. > However, some recent samples with low read counts and poor qualities > produce no contigs at all. The only thing I can think to do initially > is quality filter and try again. If anyone has compared > filtered/unfiltered assemblies I;d love to know about it. > > Jim > > ------------------------------------------------------------------------------ > Minimize network downtime and maximize team effectiveness. > Reduce network management and security costs.Learn how to hire > the most talented Cisco Certified professionals. Visit the > Employer Resources Portal > http://www.cisco.com/web/learning/employer_resources/index.html > _______________________________________________ > Denovoassembler-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/denovoassembler-users > ------------------------------------------------------------------------------ Minimize network downtime and maximize team effectiveness. Reduce network management and security costs.Learn how to hire the most talented Cisco Certified professionals. Visit the Employer Resources Portal http://www.cisco.com/web/learning/employer_resources/index.html _______________________________________________ Denovoassembler-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
