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Hi Andrea, On 26/07/13 10:05 AM, JACQUES CORBEIL wrote: > > Begin forwarded message: > >> *From: *Andrea Thuermer <[email protected] <mailto:[email protected]>> >> *Subject: **Ray meta* >> *Date: *26 July, 2013 10:02:09 AM EDT >> *To: *<[email protected] >> <mailto:[email protected]>> >> >> Dear Jacques and other co-authors of Ray meta, >> >> we are a sequencing center and some of our main scientific interests are >> microbial genomics, metagenomics and (meta)transcriptomics. That s why we >> are always interested in new assemblers. >>I was happy when i found your Ray Meta assembler. I am also happy that you found it. >> I am currently testing the it. Do you have any experience with long reads >> with your assembler? >> With -long- i think about reads >>between 2 - 10 kb, concerning the new moleculo method that illumina has >>announced?! I have not tried Moleculo reads with Ray, but I checked some reads and they very few errors like Illumina reads. I you want to test, there are these two fastq files (you just need to register on BaseSpace): https://basespace.illumina.com/sample/2354355/files/raw/mol-32-2832.fastq.gz?id=142199664 https://basespace.illumina.com/sample/2346352/files/raw/mol-32-281c.fastq.gz?id=142202448 There is also this paper http://elife.elifesciences.org/content/2/e00569/article-data with Moleculo data, but strangely the data was not released even though the paper is published ! Moleculo data for this paper should hopefully appear soo at the address http://genepyramid.stanford.edu/botryllusgenome/download/ >> Are there any experience maybe with pacBio data so far? Ray does not perform any error correction. If you use Pacific Biosciences circular consensus data, Ray will work. But for long Pacific Biosciences SMRT uncorrected data, that won't work. >> Another problem, i could not found in the manual, does the software have >> problems with the sff-files that are generated after a 454 run with flow >> pattern B? Ray has native support for sff files. However, paired reads in sff files are not extracted as pairs. I don't know what is a "pattern B" so I can answer that question I am afraid. >> I have no results >>so far, but the software did not like these sff-files as input, "old" >>sff-files before the software upgrade seem to be no problem. The implementation if based on this specification: * \see Section "13.3.8 Standard Flowgram Files (.sff)" * Genome Sequencer, Data Analysis Software Manual, Software Version 2.0.00, October 2008, page 528 * http://sequence.otago.ac.nz/download/GS_FLX_Software_Manual.pdf >> >> Thanks in advance! >> >> Best reards >> Andrea >> >> -- >> Dr. Andrea Thürmer >> - Sequencing - >> >> Universität Göttingen >> Labor für Genomanalyse >> Grisebachstraße 08 >> 37077 Göttingen >> >> email: [email protected] <mailto:[email protected]> >> Tel.: 0551/39-33841 >> >> >> > ------------------------------------------------------------------------------ See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk _______________________________________________ Denovoassembler-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
