Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • turn-key next gen companies

    I have been trying to ride the next gen sequencing tsunami for some time now. To the best of my understanding the sequencing technology is getting to a point where it is very rapidly becoming a commodity. What you do with the data once the raw sequencing data is spit out by the sequencing machines is still a bigger question in my mind. So I think any sequencing service is not complete unless the data cleaned, curated and analyzed to a minimum degree. I mean alignment and genotype and variation determination. So if you are not fortunate enough to be in one of the world excellence centers like the broad institute what are your options in terms of commercial companies that get your samples and give you a list of variants for that sample. This is similar to a clinical lab giving you the meaningful results that can be interpreted clinically compared to the raw chromatogram images that the biochemical analyzer generates. Any thoughts?

  • #2
    Hello msincan-

    I am not convinced next-gen sequencing is becoming a commodity at a rapid pace. You can find wild swings in terms of data amount, accuracy of data and quality of data from lab to lab, much more so then you can currently find in CE sequencing. However, many commercial service providers are starting to add a bioinformatics capability, although at a very basic level when compared with places like the Broad and WashU. It depends on how much curation of the data one needs. I represent a service provider so I do not want to get into specifics in this space as it would be inappropriate. If interested please tweet me at @dgaalaas.

    Comment


    • #3
      What I mean by next gen sequencing becoming a commodity is that the cost and time required to run the reactions to determine a base is becoming so little. But as I point out I do believe the challenge is still there in terms of coming up with a reliable and complete solution to give not just the sequence but the real information that comes out from analyzing the sequence.

      Comment


      • #4
        Yes, the data analysis is the rate limiting step at this point.

        There are only two commercial turn-key software analysis packages that I am aware of
        CLC Bio's Genomic Workbench and NextGene from Softgenetics.

        However, even after you analyze your data (assemble and determine variants), the next difficult step is determining the significance of those variants. This is not trivial since there are so many.

        Comment


        • #5
          Thanks NextGenSeq this is exactly the kind of discussion I was hoping to get. When you say determine the significance are you referring to methods such a s SIFT and PolyPhen or are you going one step further and talking about if the variant that has been ranked as a deleterious variant is actually causing the disease or having a significant biological/functional effect?
          I think may be galaxy may evolve into its next version that may be a viable alternative to commercial products or I am also very interested in hearing about cloud computing based solutions.

          Comment


          • #6
            There's also Partek - give it a try at www.partek.com...
            Really, in looking for a complete solution, Partek is the software to use.

            Taking RNA-Seq, Ch-IP-Seq, DNA-Seq, Methyl-Seq data from alignment, to Quality Control, to Statistical Analysis, to Biological Analysis and also to Functional Genomics by correlating data across assays -> you get a complete picture for your biological hypothesis.

            I agree the fun begins with the biological/functional effect, the visualizations in Partek report this nicely.

            Comment


            • #7
              how much does a Partek subscription cost a year? $7 million?! That can't be right.

              --
              Jeremy Leipzig
              Bioinformatics Programmer
              --
              My blog
              Twitter

              Comment


              • #8
                Ha! That's a good one!
                Partek is the most affordable commercial genomics sw to my knowledge.

                Comment


                • #9
                  Hi,

                  if you sequence your data with BGI, the bioinformatics analysis are included. And from our experience they are not only with many people, they also provide really nice curated data (even on difficult plant genomes). You can read an example in this press release: http://www.bayercropscience.com/bcsw...25764A002DE77C

                  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
                  7 views
                  0 likes
                  Last Post seqadmin  
                  Started by seqadmin, Yesterday, 06:07 PM
                  0 responses
                  7 views
                  0 likes
                  Last Post seqadmin  
                  Started by seqadmin, 03-22-2024, 10:03 AM
                  0 responses
                  49 views
                  0 likes
                  Last Post seqadmin  
                  Started by seqadmin, 03-21-2024, 07:32 AM
                  0 responses
                  66 views
                  0 likes
                  Last Post seqadmin  
                  Working...
                  X