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  • clc or dnastar

    Hi,
    Which software is more recommended for NGS analysis, array analysis, probes and primers etc, CLC or DNASTAR?

  • #2
    You can get trial licenses for most commercial software that should help you make an informed purchasing decision after you have had a chance to try the software out first-hand.

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    • #3
      CLC is far superior, particularly the new 5.5 version

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      • #4
        You also might want to look at Partek for NGS and microarray analysis. I've used it for a few years for both types of analysis.

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        • #5
          Personally I found CLC pretty but glitchy and too expensive. Unbelievably they had no facility to annotate with a .gff file except as a plugin. Did one lineup where an A and a C were considered to be 100% identical (yes, I submitted a bug report). Perhaps the new version is better? but my experience was not good. I prefer geneious, but I have to admit bias here since I'm in the same department as the devs.

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          • #6
            Obviously, I'm biased to DNASTAR, but some objective comparisons between the two (as well as other products) can be found in the following two articles recently published in BMC Genomics.

            Kumar and Blaxter: Comparing de novo assemblers for 454 transcriptome data. BMC Genomics 2010 11:571.

            Feldmeyer et al.: Short read Illumina data for the de novo assembly of a non-model snail species transcriptome (Radix balthica, Basommatophora, Pulmonata), and a comparison of assembler performance. BMC Genomics 2011 12:317.

            Both studies compared DNASTAR's SeqMan NGen with other products in performing a de novo transcriptome assembly – one study used 454 data; the other study used Illumina data - and both concluded that SeqMan NGen is the best software for performing de novo transcriptome assemblies.

            Feel free to give us a call or email if you have questions as you continue to look for software. We have a next-gen scientist dedicated to assisting with any questions you may have.

            Phone: 608-258-7420
            Toll Free in the U.S. and Canada: 866-511-5090
            [email protected]

            Thanks,
            Anne

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            • #7
              Originally posted by litali View Post
              Hi,
              Which software is more recommended for NGS analysis, array analysis, probes and primers etc, CLC or DNASTAR?
              I'd go with GenoMax.

              Give it a try yourself. If you are just asking without having some more details in mind, it is hard to tell what is best for your purpose. Keep in mind that CLC is not a transcriptome assembler, but a genome assembler and mapper ..

              cheers,
              Sven

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