Question: disadvantage of NextSeq 500 compared with MiSeq
gravatar for J.F.Jiang
5.7 years ago by
J.F.Jiang830 wrote:

Hi all,

I am comparing two platforms for our analysis, the illumine NextSeq 500 and MiSeq.

Discard of sequencing the whole genome, the price seems to be the same for the two instruments.

The advantage of Miseq is that it can get the 2x300 READS while NextSeq is 150bp.

However, the NextSeq uses a new dying system for the flow cell that it can generate more data for specific target.

What I want to know is that is there any disadvantages of Nextseq compared to Miseq?




miseq nextseq • 9.8k views
ADD COMMENTlink modified 5.7 years ago by chopranik10 • written 5.7 years ago by J.F.Jiang830
gravatar for Asaf
5.7 years ago by
Asaf8.3k wrote:

I don't have experience with miSeq but in NextSeq runs I analyzed, if you put too much DNA on the flow-cell and have a lot of reads (600M) the paired (second) reads are very often poly-G (up to 20% of the reads! G meaning no color) or just low quality, I had to throw them away several times. Even with low number of reads you get 1-2% poly-G on the second read.

Using the NextSeq is pretty easy, you bring your kit, punch some holes, drop your DNA and you're ready to go, this can be a consideration when you're buying a machine a lot of people will want to use, you don't need to have a dedicated technician. Another issue is that you can join several samples (from different labs) in the same run instead of waiting in line, all you need is to use different sets of barcodes.

ADD COMMENTlink written 5.7 years ago by Asaf8.3k


Totally with you comments.

Discard of the inaccuracy of the results (compared to MiSeq), after couple of improvement, NextSeq might replace MiSeq platform to become the best instrument to sequence both targets and whole genome.


ADD REPLYlink written 5.7 years ago by J.F.Jiang830

We went back and check the amount of DNA poured onto flowcell. The amount seems to be reasonable. Could this be caused by any other reason? Besides, why excessive amount of DNA on flowcell would cause this?

ADD REPLYlink written 2.5 years ago by CY510
gravatar for Brian Bushnell
5.7 years ago by
Walnut Creek, USA
Brian Bushnell17k wrote:

NextSeq currently has substantially lower accuracy than MiSeq.  I would not recommend it unless you are doing something purely quantitative.

ADD COMMENTlink written 5.7 years ago by Brian Bushnell17k

ADD REPLYlink written 5.2 years ago by dsbreak150

Nextseq has been used in clinical settings. The base calling accuracy is not everything, only the end result matters. QC comparison can be found here

ADD REPLYlink written 4.3 years ago by Jussi180
gravatar for dariober
5.7 years ago by
WCIP | Glasgow | UK
dariober11k wrote:

A couple of comments, which might be outdated:

  • The cost per run is lower for the MiSeq (although the cost per base is higher)
  • The sequence quality of the MiSeq is generally higher.
  • As you say, the NextSeq has a different system and as such there are more unknowns.

In my experience the NextSeq is a great device anyway.

ADD COMMENTlink written 5.7 years ago by dariober11k

Thanks, great comment.

ADD REPLYlink written 5.7 years ago by J.F.Jiang830
gravatar for chopranik
5.7 years ago by
United States
chopranik10 wrote:

Good to know, I am analyzing a Nextseq run as well and see expected straight line of G's at the end of the read. How much would you believe the CD calculations in the summary if the loading is very high

ADD COMMENTlink modified 5.7 years ago • written 5.7 years ago by chopranik10
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