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  • de novo assembly on 3.5Gbp data -- computational speed!!??

    i have used Velvet & SSAKE to build some contigs before and found that they can't take more than 10 million reads (75bp each) (it just gets really really slow beyond that)

    but now i need to do a de novo assembly using much more than 10 mill reads (45mill reads/ 3.5Gbp). HOW am i going to do it? or should i just expect the program to finish in months instead in hours?

    thx
    jason

  • #2
    Are you working with paired-end reads or any usable mate-pair information?

    Comment


    • #3
      Just illumina data
      1 set of 75bp paired end reads
      1 set of 35bp paired end reads
      and 1 set of single end 75bp reads

      Comment


      • #4
        Originally posted by jtjli View Post
        i have used Velvet & SSAKE to build some contigs before and found that they can't take more than 10 million reads (75bp each) (it just gets really really slow beyond that)

        but now i need to do a de novo assembly using much more than 10 mill reads (45mill reads/ 3.5Gbp). HOW am i going to do it? or should i just expect the program to finish in months instead in hours?

        thx
        jason
        Wow, I did not know of such a limit to number of reads for velvet!
        Did you check with velvet's author?
        --
        bioinfosm

        Comment


        • #5
          yes i did.
          i think that is more a problem of my 16GB ram limitation.
          Nothing wrong with velvet (ssake is similar)

          i'm just hoping someone can shed me some light on this

          Comment


          • #6
            maybe you can try Edena

            De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer.
            D. Hernandez, P. François, L. Farinelli, M. Osteras, and J. Schrenzel.
            Genome Research. 18:802-809, 2008.


            http://www.genomic.ch/edena.php

            Comment


            • #7
              just read the quickTutorial of Edena, it doesn't seem to work with paired end reads??

              Comment


              • #8
                Hello Jason,

                Have you tried Abyss?

                http://www.bcgsc.ca/platform/bioinfo/software/abyss

                Comment


                • #9
                  I just posted a new version of euler-sr. It should run with less memory, so it will be less likely to start paging. The webpage is euler-assembler.ucsd.edu/portal

                  -mark

                  Comment


                  • #10
                    Originally posted by mchaisso View Post
                    I just posted a new version of euler-sr. It should run with less memory, so it will be less likely to start paging. The webpage is euler-assembler.ucsd.edu/portal

                    -mark
                    Are there some numbers on 'less' memory?

                    Thoughts on assembling human scale genomes? any appropriate tools?
                    --
                    bioinfosm

                    Comment

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