Hello, On 04/04/13 04:57 PM, Hung-Ying Lin wrote: > Dear Dr. Boisvert,
I am not a doctor. > > Please allow me to introduce myself. I'm Hung-Ying, currently a PhD > student in Genetics program at Iowa State University and I am conducting a > project that compares > performances among several assemblers using simulated illumina datasets. > By performance, do you mean assembly quality and things like that or you mean speed, scalability and memory usage. Or do you mean ease of use ? > The project was almost completed. But to make sure I've tried sufficient > numbers of parameter combinations and reach its optimum, I would like to have > some >comments directly from the authors. That's a good idea. > The attachment is the result I have so far. There is no attachment. > Would you be willing to take a look and give me some suggestions. > Sure, > > An additional question about the algorithm or mechanism behind hybrid > assembly in Ray. I have searched your papers, it mentioned Ray can support > hybrid assembly, > however I don't find any command in user manual. Ray can use various sequencing technologies because it builds the de Bruijn graph using all k-mers from every sequence. Also, various heuristics are used to browse the graph: paired reads, mate pairs, read threading, tip detection, and so on. > Does it mean Ray can detect the length automatically? Ray detects automatically (i.e. auto-calibration of paired read outer distance distributions). > How can I deal with hybrid assembly(illumina + 454 and illumina + >contigs sequence) in Ray? Just provide every file you have either as single-end reads (with -s file.fastq) or as paired-end reads (with -p file1.fastq file2.fastq). > > > Thank you in advance for your replying, your commons will be very important > to me and have a nice day. > > Sincerely, > Hung-Ying > ------------------------------------------------------------------------------ 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 Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
