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  • bioman1
    Member
    • May 2012
    • 80
    #1

    Minia-genome assembler

    Hello,

    I am working in the plant genome assembly. I am working on workstation, my fastq file (interleaved as single fastq file) is about 120Gb. I cannot able use velvet, soapdenovo due to memory constraint. I am trying to assemble with minia, which uses very low memory. Although, minina give comparable N50 to other frequently used genome assembler. I wonder why this assembler not used much in genome assembly project?. If I use this assembler, do I have any problem in publication?
    Tags: genome assembly minia
  • WhatsOEver
    Senior Member
    • Apr 2012
    • 215
    #2
    You probably haven't seen the publication of the assembler, have you? (Space-efficient and exact de Bruijn graph representation based on a Bloom filter, http://www.almob.org/content/8/1/22)

    Though the impact factor of ABM is quite low, it is peer-reviewed, so you shouldn't have any problems when using it.
    The reason why it hasn't been cited much is probably that it is quite new?!

    Comment

    • rchikhi
      Member
      • Jan 2013
      • 11
      #3
      As an author, I also wonder why

      You should have no problem submitting the results of a Minia assembly to a conference/journal. Actually, if anyone feels otherwise, please state your concern (the software is still actively supported by its authors).
      Last edited by rchikhi; 07-24-2014, 10:22 AM.

      Comment

      • samanta
        Senior Member
        • Feb 2010
        • 108
        #4
        The first rule of using Minia assembler: You do not talk about Minia assembler.

        The second rule of using Minia assembler: You do not talk about Minia assembler.

        Third rule of using Minia assembler: Someone yells stop, goes limp, taps out, the assembly is over.

        Fourth rule: assemble only large genomes with Minia, take wimpy bacterial ones to Velvet.

        Fifth rule: one assembly at a time, fellas.

        Sixth rule: no 512GB servers, no digital normalization.

        Seventh rule: Assembly will go on as long as they have to.

        And the eighth and final rule: If this is your first time assembling large genomes, you have to use Minia assembler.
        http://homolog.us

        Comment

        • zs_03
          Junior Member
          • Dec 2015
          • 1
          #5
          Can anyone tell me how to install minia software?

          Comment

          • rchikhi
            Member
            • Jan 2013
            • 11
            #6
            If you run linux 64 bits, then the binary is available here: http://minia.genouest.org/
            Sources can be compiled too from there, but it takes a bit more effort.

            Comment

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