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  • Cloud-MAQ

    We have developed an enhanced version of MAQ called Cloud-MAQ. It outperforms MAQ in terms of runtime. For 120 million (33 base, Illumina) sequence reads on a single core, MAQ took 8hrs for reference assembly. While Cloud-MAQ on the same data set took 53mins using 4 cores. I can share more information and the software for anybody who is interested in trying our version...

  • #2
    Moved this to its own thread as it is clearly not a package available for use today, but definitely worthy of discussion.

    Link to amazon image so I can try it?

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    • #3
      Originally posted by geschickten View Post
      We have developed an enhanced version of MAQ called Cloud-MAQ. It outperforms MAQ in terms of runtime. For 120 million (33 base, Illumina) sequence reads on a single core, MAQ took 8hrs for reference assembly. While Cloud-MAQ on the same data set took 53mins using 4 cores. I can share more information and the software for anybody who is interested in trying our version...
      Could you post a link to the software? Is it free?

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      • #4
        Originally posted by geschickten View Post
        I can share more information and the software for anybody who is interested in trying our version...
        Here! Here! Definitely interested!

        Best
        -Jonathan

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        • #5
          I will post the link soon. We are in the last leg of quality testing...thank you

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          • #6
            I also would like a test on it. Thanks

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            • #7
              good new

              post the linker,please

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              • #8
                We will post the link on our website soon after holidays. Thank you and Happy Holidays to you all....

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                • #9
                  I am pleased to announce that Cloud-MAQ is available for download. For enthusiasts please go to http://www.geschickten.com/PaCGeE.html.

                  Please remember that your suggestions and feedback are always appreciated. Thank you.

                  Prahalad

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                  • #10
                    Originally posted by geschickten View Post
                    I am pleased to announce that Cloud-MAQ is available for download. For enthusiasts please go to http://www.geschickten.com/PaCGeE.html.

                    Please remember that your suggestions and feedback are always appreciated. Thank you.

                    Prahalad
                    Is the MAQ you created based on the source code of MAQ found on sourceforge.net? Are you going to release the source code?

                    Comment


                    • #11
                      I've yet to run it;
                      but from what I have seen from a short analysis of the contained python-c apps, this looks like a wrapper-approach for the usual maq map step to utilize the hadoop storage, map and reduce algorithms.

                      But that's just a quick take, and I assume that since its a requirement to have maq 0.6.8 (why not the latest 0.7.x???) and maqview installed, that this will likely stay closed source - otherwise all the hassle with the download, like asking for a phonenumber+email wouldn't have been necessary.

                      These are my 5 cents, but I'd like to be proven wrong,
                      Best
                      -Jonathan

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                      • #12
                        nilshomer & Jonathan

                        I know its a pain to pen a few details before you download any softwareand I am sorry for that; well Jonathan you are partially right; I mean what we have is a wrapper and we have not modified the source of MAQ; The reason we suggest 0.6.8 is because MAQ 0.7.x is a little inconsistent and there are issues with MAQVIEW too. Hence we restricted ourselves to 0.6.8; but that will change in future. Thank you.

                        Prahalad

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                        • #13
                          Originally posted by geschickten View Post
                          nilshomer & Jonathan

                          I know its a pain to pen a few details before you download any softwareand I am sorry for that; well Jonathan you are partially right; I mean what we have is a wrapper and we have not modified the source of MAQ; The reason we suggest 0.6.8 is because MAQ 0.7.x is a little inconsistent and there are issues with MAQVIEW too. Hence we restricted ourselves to 0.6.8; but that will change in future. Thank you.

                          Prahalad
                          Are you distributing MAQ with your code or do you have to download it yourself?

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                          • #14
                            We are not distributing MAQ; you have to download it from sourceforge. The README in the distribution has all the details. Thanks

                            -p

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                            • #15
                              Hi,

                              does it still works with MAQ 0.6.8 ?

                              I'm new to the field, and I wanted to run it on IBM clusters. This seems to be the solution. is source code available?

                              does anyone know if the results are different than just running MAQ ?

                              Comment

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