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  • sklages
    replied
    Hi Gabriel,

    Originally posted by gabriel.lichtenstein View Post
    Hi there,

    I 've requested Roche a software copy from their support page, hope they consider sending me the DVD's to Argentina.

    Having this in mind I wanted to ask in the forum wich alternative would you recommend me for de novo genome assembly using roche's 454 .sff files.

    Celera, CLC, Velvet, GenomeQuest, Arachne, etc?
    Depends on what you are expecting and if you are willing to spend (a lot) of money for software ...

    Celera works fine if you have PE libraries, final result can be converted to ace which can be edited with consed. We are working on a CAF converter as well. CLC may work fine as well, cost a lot of money, ace export is poor. I'd only use velvet for short reads, not for 454 and/or sanger data, but that is my personal opinion ;-)
    You might also want to have a look at MIRA3 (http://chevreux.org/projects_mira.html).


    Issue#2: Any ideas from where I could get a pipeline procedure for cleaning (trimming) the 454 files in order to prepare the seqs for assembly.
    What do you want to trim? The quality trimming is usually done by the roche software itself. If you have a genomic library there should not be too much to clip off ...

    cheers from lima/peru (just for vacation, sigh),
    Sven

    Leave a comment:


  • gabriel.lichtenstein
    replied
    Hi there,

    I 've requested Roche a software copy from their support page, hope they consider sending me the DVD's to Argentina.

    Having this in mind I wanted to ask in the forum wich alternative would you recommend me for de novo genome assembly using roche's 454 .sff files.

    Celera, CLC, Velvet, GenomeQuest, Arachne, etc?

    Issue#2: Any ideas from where I could get a pipeline procedure for cleaning (trimming) the 454 files in order to prepare the seqs for assembly.

    Thank you very much for any information,

    Wish you all a Merry Xmas and a Happy new year

    Best Regards,

    Gabriel

    P.S: It's a Plant Genome.

    Leave a comment:


  • gabriel.lichtenstein
    replied
    Newbler DvD's

    Hi there,

    I had the same problem here in Argentina, I was wondering if maybe someone could ship me a copy of the Newbler DVD's. I would of course pay for the shipping costs and the copy.
    If possible, please send me an email.

    Thank you very much

    Leave a comment:


  • maubp
    replied
    Another positive example: we asked about this via our local sequencing centre (in the UK), and Roche was happy for them to make Newbler available to us and other users.

    Did you have any progress with Roche's Chile representatives srcam?

    Leave a comment:


  • AlexB
    replied
    Hey
    the same here for me (in the Netherlands). I didn't even ask for the software but since our University already had an older (GLX) one and now have a Titanium..... They just asked whether the software might be useful to have.... of course ... next day the DVDs and 3 days later the thick manual in print on my desk
    For large assemblies I think you need quite a strong linux computer though...
    Alex

    Leave a comment:


  • sram
    replied
    Originally posted by strob View Post
    I work indeed in Belgium, Europe. And I even work in a commercial company....

    At the PAG meeting I discussed this with Roche at their booth and they just told me that I should contact my local contact. After 1 phone cal, I received the software.
    OK. So I don't understand my experience with Roche here in Chile.
    Thank you for your message.
    Regards,

    ---sram

    Leave a comment:


  • sram
    replied
    Originally posted by strob View Post
    Again, I had no trouble getting the software. They just asked me where we get our sequences from (which provider), and a few days later the DVD's were in my mailbox....
    Perhaps different policy for latin america?
    I received the answer from:

    Head
    Roche Applied Science
    Roche Diagnostics Chile

    However he asked me to write a letter to justify why I need the software and for what. I find this quite annoying since I can't imagine another use but to assemble DNA sequences. Anyway...

    ---sram
    Last edited by sram; 09-11-2009, 05:08 AM.

    Leave a comment:


  • strob
    replied
    I work indeed in Belgium, Europe. And I even work in a commercial company....

    At the PAG meeting I discussed this with Roche at their booth and they just told me that I should contact my local contact. After 1 phone cal, I received the software.

    Leave a comment:


  • sram
    replied
    Originally posted by dan View Post
    I really have no idea why Roche insist that only people with the sequencer are allowed the software... They are actively damaging their software's status among the bioinformatics community.

    Seriously, what do they expect? Only sequencing centres will do bioinf analysis with 454 data? Clearly not. Therefore we are forced by Roche NOT to use Roche products... What kind of crazy logic is that?

    Dear Roche,

    Please make Newbler open source immediately.

    Sincerely,

    Someone who imagines that you actually care about improving your software and increasing its user base.


    sram, try writing to the people who gave you the data, and ask them to ask Roach on your behalf.
    Dan, thank you. I will do that. I am receiving the data from research centres in Europe who work with us in some projects. In fact some samples are ours and they are supporting us with the sequencing. Perhaps Roche have a different policy in Europe.. taking in account the message from strob, who appear to be writing from Belgium.
    I totally agree with you about Roche should make this software available for academic research. For commercial uses is another thing.

    ---sram

    Leave a comment:


  • strob
    replied
    Again, I had no trouble getting the software. They just asked me where we get our sequences from (which provider), and a few days later the DVD's were in my mailbox....

    Leave a comment:


  • dan
    replied
    I really have no idea why Roche insist that only people with the sequencer are allowed the software... They are actively damaging their software's status among the bioinformatics community.

    Seriously, what do they expect? Only sequencing centres will do bioinf analysis with 454 data? Clearly not. Therefore we are forced by Roche NOT to use Roche products... What kind of crazy logic is that?

    Dear Roche,

    Please make Newbler open source immediately.

    Sincerely,

    Someone who imagines that you actually care about improving your software and increasing its user base.


    sram, try writing to the people who gave you the data, and ask them to ask Roach on your behalf.

    Leave a comment:


  • sram
    replied
    Not so here in Chile...

    Originally posted by strob View Post
    If you use 454 data you can just ask for the Newbler software. We did it this way and we received a DVD containing everything we need.
    I did that and I was told I can get the software only if I have a GS FLX system. I get this answer from a representant of Roche here in Chile.

    ---sram

    Leave a comment:


  • v_kisand
    replied
    MIRA should be nice alternative as well. I would go on wgs or MIRA ... or check velvet... in my mind these three are the most promising. I tested a bit CLC Genome Workbench and was not particularly impressed...

    Originally posted by strob View Post
    If you use 454 data you can just ask for the Newbler software. We did it this way and we received a DVD containing everything we need.

    Leave a comment:


  • strob
    replied
    If you use 454 data you can just ask for the Newbler software. We did it this way and we received a DVD containing everything we need.

    Leave a comment:


  • sklages
    replied
    wgs-assembler makes a good job on sanger, FLX and Titanium data either alone
    or as hybrid assemblies ..

    It is not working with short read data (illiumina, solid) and is not optimised for
    old gs20 data.

    cheers,
    Sven

    Leave a comment:

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