Dear Sebastien, thanks a lot, that was really helpful! Our first testassemblies with ray are very promising!
best regards Andrea Thürmer On 26.7.13 16:55, Sébastien Boisvert wrote: > [Please use the mailing list, to subscribe: > http://lists.sourceforge.net/lists/listinfo/denovoassembler-users ] > > > Hi Andrea, > > On 26/07/13 10:05 AM, JACQUES CORBEIL wrote: >> >> Begin forwarded message: >> >>> *From: *Andrea Thuermer <athu...@gwdg.de <mailto:athu...@gwdg.de>> >>> *Subject: **Ray meta* >>> *Date: *26 July, 2013 10:02:09 AM EDT >>> *To: *<jacques.corb...@crchul.ulaval.ca >>> <mailto:jacques.corb...@crchul.ulaval.ca>> >>> >>> 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: athu...@gwdg.de <mailto:athu...@gwdg.de> >>> Tel.: 0551/39-33841 >>> >>> >>> >> > -- Dr. Andrea Thürmer - Sequencing - Universität Göttingen Labor für Genomanalyse Grisebachstraße 08 37077 Göttingen email: athu...@gwdg.de Tel.: 0551/39-33841 ------------------------------------------------------------------------------ Get your SQL database under version control now! Version control is standard for application code, but databases havent caught up. So what steps can you take to put your SQL databases under version control? Why should you start doing it? Read more to find out. http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
