Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Free NGS 1x50 SE rapid run

    Hi All,

    I have one Free Rapid 1x50 SE run to qualify my recently acquired HiSeq 2500. I thought it will be shame to waste it with PhX control, so I am open to hear your ideas and proposals for sequencing your library and why it will be interesting do so. It is absolutely free and there are no guarantees, however there is good chance to get some free data.


    If you want to get in touch visit hera-bio (dot) com

    Cheers,
    Peter

  • #2
    For qualification purposes, I think PhiX is a bit too simple, and a bad choice anyway because Illumina's calibration is PhiX-based. That said, human is also bad because it's diploid and highly variable which makes it harder to distinguish between variations and errors.

    Though it's tempting to try to run an experiment during validation (and we do that all the time at JGI), I highly encourage you to resist the temptation! Rather, sequence multiplexed E.coli + something else completely different. Then you can calculate error rates, quality score accuracy, cross-contamination rates, insert-size distributions, GC and coverage-bias, and all the metrics you could ever want, without conflating factors that come from experiments.

    Comment


    • #3
      Brian, thanks for your input. I will spike in some e-coli libraries that I already sequenced, however I still can fit in an experiment given the e.coli can be small fraction.
      Thanks again.
      Peter

      Comment


      • #4
        You bought a HS2500? I thought the machine was being discontinued by Illumina.
        Don't get me wrong: the machine itself is awesome, very flexible with high quality runs. We are using one for more than 3 years and are very happy with it.
        It's just that the sequencing price is higher than what can offer a 3000 or 4000 (let's not talk about Novaseq). And as Illumina discontinued it (or at least, that's what our sale representative told us so), you might not expect new improvments on it.

        Comment


        • #5
          I'd still greatly prefer HS2500 over HS3000/4000... cost aside, it outperforms them in all my quality-related tests.

          Comment


          • #6
            Originally posted by huguesparri View Post
            You bought a HS2500? I thought the machine was being discontinued by Illumina.
            I don't think so. It is still prominently listed on Illumina's site. It is a workhorse and probably one of the best sequencers Illumina has ever made.

            Comment


            • #7
              I agree with both of you regarding the quality of the machine itself. As I said, we have one for 3 years now and we are completely satisfied with it (set aside the price of the reagents).
              But as previously said, our sale representative told us that Illumina was planning to discontinue it as well as Hiseq3000. Maybe she was wrong, or maybe Illumina did change their mind (or maybe they only plan to do it later...).

              Comment


              • #8
                Originally posted by huguesparri View Post
                You bought a HS2500? I thought the machine was being discontinued by Illumina.
                Don't get me wrong: the machine itself is awesome, very flexible with high quality runs. We are using one for more than 3 years and are very happy with it.
                It's just that the sequencing price is higher than what can offer a 3000 or 4000 (let's not talk about Novaseq). And as Illumina discontinued it (or at least, that's what our sale representative told us so), you might not expect new improvments on it.
                HiSeq 2500 is still the best machine out there (in my opinion).
                Quality/price I paid = no brainer

                Comment

                Latest Articles

                Collapse

                • 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
                • seqadmin
                  The Impact of AI in Genomic Medicine
                  by seqadmin



                  Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
                  02-26-2024, 02:07 PM

                ad_right_rmr

                Collapse

                News

                Collapse

                Topics Statistics Last Post
                Started by seqadmin, 03-14-2024, 06:13 AM
                0 responses
                33 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 03-08-2024, 08:03 AM
                0 responses
                72 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 03-07-2024, 08:13 AM
                0 responses
                80 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 03-06-2024, 09:51 AM
                0 responses
                68 views
                0 likes
                Last Post seqadmin  
                Working...
                X