Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • PacBio RS latest specs anyone?

    Hi All

    With a few units now out there has anyone got any data parametrics to share. What read lengths are you getting using each of the opration modes. Has the raw read accuracy increased? To what? We are talking in the field experience rather than company specs.

    Cheers

  • #2
    Are there even recent company specs posted anywhere?

    Comment


    • #3
      We are getting post-filter mean read lengths of between 1.5 - 2.0 kb and between 25-40K reads per SMRTcell. We have mainly done just standard sequencing and "filter only" analysis at the moment.


      Originally posted by markwatson View Post
      Hi All

      With a few units now out there has anyone got any data parametrics to share. What read lengths are you getting using each of the opration modes. Has the raw read accuracy increased? To what? We are talking in the field experience rather than company specs.

      Cheers

      Comment


      • #4
        Out of interest, how long do you have to run the machine to yield an average read length of 1.5-2kb?

        Comment


        • #5
          And what ballpark cost is it per run?

          Comment


          • #6
            We are doing 2 x 45 min runs, so 90 min per SMRTcell.

            Originally posted by myrna View Post
            Out of interest, how long do you have to run the machine to yield an average read length of 1.5-2kb?

            Comment


            • #7
              Originally posted by GenoMax View Post
              We are getting post-filter mean read lengths of between 1.5 - 2.0 kb and between 25-40K reads per SMRTcell. We have mainly done just standard sequencing and "filter only" analysis at the moment.
              What is your overall impression of PacBio RS? What are the pros and cons you have seen? If you can, how would you compare it to other technologies?

              Comment


              • #8
                It is a little early to say something definitive.

                This is a relatively young company that is trying to succeed (the layoffs reported yesterday should give people something to think about though) in the world of Illumina/ABI.

                I do not work on the "wet-bench" side of things so can't comment on how easy/difficult things are.

                PacBio made some design decisions on the SMRTanalysis package ("primary" analysis happens on the cluster associated with the instrument, end-users have no access to this part) software that may or may not work for all (I suppose they had to start somewhere). This is an area that needs improvement and polish (e.g. currently no quality scores (so no fastq) can be had for sequence data by default). Hopefully these are temporary inconveniences that will be addressed in due course of time.

                Originally posted by clostridium40 View Post
                What is your overall impression of PacBio RS? What are the pros and cons you have seen? If you can, how would you compare it to other technologies?

                Comment


                • #9
                  Hi GenoMax

                  Thank you for your feedback on the software. I wanted to let you know that you can set the software to produce fastq files by default by using the RS Remote software and setting up a preference for what outputs you would like to automatically produce. One of the options provided as a checkbox is fastq.

                  Comment


                  • #10
                    I was referring to the "final" sequence file produced at the end of "secondary" analysis. With SMRTanalysis v.1.2.1 this is not possible.


                    Originally posted by pacbio View Post
                    Hi GenoMax

                    Thank you for your feedback on the software. I wanted to let you know that you can set the software to produce fastq files by default by using the RS Remote software and setting up a preference for what outputs you would like to automatically produce. One of the options provided as a checkbox is fastq.

                    Comment


                    • #11
                      Originally posted by GenoMax View Post
                      I was referring to the "final" sequence file produced at the end of "secondary" analysis. With SMRTanalysis v.1.2.1 this is not possible.
                      Thanks for the clarification. With the current version of SMRT Analysis, we offer BAM as an output which contain the consensus call QVs. To get at fastq, you will need to use post processing scripts, Picard, etc. However, we will add this feature request.

                      Thanks again.

                      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
                      9 views
                      0 likes
                      Last Post seqadmin  
                      Started by seqadmin, 03-22-2024, 10:03 AM
                      0 responses
                      50 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