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  • Analyzing NGS-data for dummies/biologists: suggestions for software?

    Hello everybody,

    In our department we are currently working with next-generation sequencing methods (mainly 454) to sequence microbial genomes and are also aiming to do ChIP-seq and RNA-seq experiments (with Illumina and SOLiD) in prokaryotes.
    For the analysis of sequences we rely on ad hoc collaborations with bioinformaticians but we would prefer to do these analyses ourselves. However, we have no experience in programming or scripting. So does anybody know if there is software available (freeware or commercial) that we could test to see if it would work for our applications?
    We will be testing CLC Genomics Workbench in the coming weeks. Does anybody want to share experiences about this particular software package? And feel free to suggest any other easy-to-work-with alternatives!

  • #2
    CLC Bio's Genomic Workbench is very easy to use and if you purchase their Genomics Machine incredibly fast. I've used it with Illumina data and have been impressed. We will be testing it with SOLiD data next week.

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    • #3
      Disclosure: I used to work for Gene Codes

      Has anyone used Sequencher for Nextgen analysis?

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      • #4
        I used to use Sequencher for 3700 data and unless Sequencher has improved dramatically in the past 5 years, CLC Bio is light years ahead.

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        • #5
          Hi,
          Have you tried NextGene software http://www.softgenetics.com/NextGENe.html
          it's running under windows and need no programming skills.
          it's available for trial in the link provided.
          Regards,
          Ramzi
          Research Scientist - Bioinformatics
          Sidra Medical and Research Center

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          • #6
            Hi MicroOmicsMan,

            Well you may not need to know programming or scripting to use any tools; but NGS data analysis according to me is more computational than biology and hence it always helps if you know programming. Well to make things a little easy and use commodity machines instead of expensive computing machines for Genomics, we have developed a Hadoop based reference assembly software called Cloud-MAQ; you can use our software on your existing machines and still get superior performance. If interested I can send you the link for you to download our evaluation copy.

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            • #7
              Originally posted by geschickten View Post
              Hi MicroOmicsMan,

              Well you may not need to know programming or scripting to use any tools; but NGS data analysis according to me is more computational than biology and hence it always helps if you know programming. Well to make things a little easy and use commodity machines instead of expensive computing machines for Genomics, we have developed a Hadoop based reference assembly software called Cloud-MAQ; you can use our software on your existing machines and still get superior performance. If interested I can send you the link for you to download our evaluation copy.
              Can you please post the link to Cloud-MAQ? I believe many people have been asking for it. Is it free? I would assume so since MAQ is GPL.

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