Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Minimum run output and quality

    Hello,

    I hope this is the right place to ask this.

    I was asked to write the terms for a tender for a NGS service provider for our institute.

    We aim to work mainly with whole genome sequencing/re-sequencing of bacteria and viruses.

    The question is how may I specify the minimum parameters of output and quality below which it would be reasonable to require (demand?) that the service provider perform a run again without charge?

    I mean, what is the minimum % of the expected output for any type of run (say, Illumina) below which a run is considered invalid? Same for average quality? Other parameters that should be included (run parameters)?

    Thank you!

  • #2
    Take a look at http://allseq.com/ and https://genohub.com/ to get an idea of what is out there. The guarantee's are going to vary from provider to provider.

    Yields from typical Illumina runs are published in the specs for each instrument (e.g. http://www.illumina.com/systems/hise...fications.html you can search for other sequencers). You need to keep in mind that these specs are for "normal" (uniform A/C/T/G distribution) samples and while they are achievable with regular samples the quality of the libraries has to be excellent to get this sort of output. You have not said if you will be making the libraries or expect the provider to make them. Quality libraries will generate quality output.

    Ultimately the level of service may depend of the volume of samples you have available. Larger volumes will give your more flexibility. But if the volume is low then don't expect a lot of leeway.

    Comment


    • #3
      Hi,

      Thanks for the links. From Genohub:

      Unless otherwise specified in the quote, the provider agrees to deliver pass filter reads that are at least 85%.
      So, if I got it right, let's say we are talking about a Miseq run with V2 chemistry. Illumina specs. are
      >75% bases higher than Q30 at 2x250 bp
      . So the sequencer in Genohub would guarantee for minimum 85% or of the 75% expected output?

      Comment


      • #4
        Oh, and I mean that lib prep would be included in the service.

        Comment


        • #5
          Originally posted by sebl View Post
          Hi,

          So, if I got it right, let's say we are talking about a Miseq run with V2 chemistry. Illumina specs. are . So the sequencer in Genohub would guarantee for minimum 85% or of the 75% expected output?
          Yes. Achievable with normal/good libraries (no low nucleotide diversity).

          Be sure to include sample QC in your request since that will likely be an added cost. It may sometimes be worth paying that upfront since you will know which samples are not worth processing for libraries.

          Comment


          • #6
            Good point, thanks!

            Comment

            Latest Articles

            Collapse

            • seqadmin
              Current Approaches to Protein Sequencing
              by seqadmin


              Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
              04-04-2024, 04:25 PM
            • 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

            ad_right_rmr

            Collapse

            News

            Collapse

            Topics Statistics Last Post
            Started by seqadmin, 04-11-2024, 12:08 PM
            0 responses
            17 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 04-10-2024, 10:19 PM
            0 responses
            21 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 04-10-2024, 09:21 AM
            0 responses
            16 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 04-04-2024, 09:00 AM
            0 responses
            46 views
            0 likes
            Last Post seqadmin  
            Working...
            X