Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • sebl
    replied
    Good point, thanks!

    Leave a comment:


  • GenoMax
    replied
    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.

    Leave a comment:


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

    Leave a comment:


  • sebl
    replied
    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?

    Leave a comment:


  • GenoMax
    replied
    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.

    Leave a comment:


  • sebl
    started a topic Minimum run output and quality

    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!

Latest Articles

Collapse

  • seqadmin
    Recent Advances in Sequencing Analysis Tools
    by seqadmin


    The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
    05-06-2024, 07:48 AM
  • seqadmin
    Essential Discoveries and Tools in Epitranscriptomics
    by seqadmin




    The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...
    04-22-2024, 07:01 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 05-14-2024, 07:03 AM
0 responses
27 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-10-2024, 06:35 AM
0 responses
47 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-09-2024, 02:46 PM
0 responses
59 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-07-2024, 06:57 AM
0 responses
47 views
0 likes
Last Post seqadmin  
Working...
X