Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Hello - Anyone ever used Geneious?!

    New to SeqAnswers so hello...? Found some posts about Geneious and they said something about having server capabilities with Bowtie, Maq and it's own assembler...

    Any Thoughts?

    Cheers

  • #2
    Welcome Jeremy,

    I'm going to guess that your post will get more eyes in the Bioinformatics forum...so I'm moving it there.

    Comment


    • #3
      I have a full license to Geneious. It is a great (arguably the best all-inclusive) genomics and phylogenetics package on the market.

      That being said, it is relatively costly and you can accomplish much (if not all) of what it does using free software. That's how it always goes with pay vs. free software.

      So I would say it really is more of a fiscal issue than a technical one.

      Specifically for your alignment question I have actually never used Geneious for this. I prefer the command line which allows for much more rapid paramater changing and piping.

      Feel free to email me if you have any specific questions.

      SAH

      Comment


      • #4
        Geneious

        Hi Jeremy

        I began using Geneious Pro last year when I began work on an Illumina GE machine. I had minimal bioinformatics experience other than alignments and trees. I found it easy to use for de novo assembly of contigs and to batch blast them. It gave me nice graphics that I have used in several publications that arose from the work. Most of what it does is freely available as command line programs, but it does most of what I need in the one package. I use an iMac and it runs well on their Snow Leopard OS.

        It is probably not right for you if you are a whiz with perl and unix but for the biologist who is thrown in the deep end with 40 million reads to analyse, I highly recommend it.

        Comment


        • #5
          Hi,

          I have a Geneious license and before deciding which integrated solution I would select, I tested also CLC Genomics, DNAstar, and NextGene solutions. Among all I decided for Geneious. Nonetheless, I do expect some improvements in the next release (which should be soon). For instance, I am not very happy with their ngs assembler and in fact I dedicated part of my time learning linux basics to use several free bioinfo tools. In my opinion (although I'm a biologist) is not so difficult to "compile/use" many of the available tools which gives very high quality results.(in other cases you run into hard successive errors...ouch).
          In sum, I would advise Geneious however, at a certain point you might find important/crucial to explore/learn other tools

          Comment


          • #6
            Wow, I keep hearing that...

            I keep hearing that... that everyone basically loves Geneious but they have to learn how to use the freeware either way... I believe Geneious has Bowtie in it and a Geneious Server that can run NGS stuff on clusters... well, thanks for the feedback!

            JaRu


            Originally posted by Pedro View Post
            Hi,

            I have a Geneious license and before deciding which integrated solution I would select, I tested also CLC Genomics, DNAstar, and NextGene solutions. Among all I decided for Geneious. Nonetheless, I do expect some improvements in the next release (which should be soon). For instance, I am not very happy with their ngs assembler and in fact I dedicated part of my time learning linux basics to use several free bioinfo tools. In my opinion (although I'm a biologist) is not so difficult to "compile/use" many of the available tools which gives very high quality results.(in other cases you run into hard successive errors...ouch).
            In sum, I would advise Geneious however, at a certain point you might find important/crucial to explore/learn other tools

            Comment

            Latest Articles

            Collapse

            • seqadmin
              Strategies for Sequencing Challenging Samples
              by seqadmin


              Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
              03-22-2024, 06:39 AM
            • seqadmin
              Techniques and Challenges in Conservation Genomics
              by seqadmin



              The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

              Avian Conservation
              Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
              03-08-2024, 10:41 AM

            ad_right_rmr

            Collapse

            News

            Collapse

            Topics Statistics Last Post
            Started by seqadmin, Yesterday, 06:37 PM
            0 responses
            10 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, Yesterday, 06:07 PM
            0 responses
            10 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 03-22-2024, 10:03 AM
            0 responses
            51 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 03-21-2024, 07:32 AM
            0 responses
            67 views
            0 likes
            Last Post seqadmin  
            Working...
            X