I would like to know what are the main limitations of using nanopore sequencing, what are the most difficult steps ?
How about support, applications available (are apps easy to use and free of charge ?).
Are the real costs of using nanopore are smaller or bigger than illumina's solutions ?
I have experience in Illumina sequencing, but I wonder if nanopore technology is a real competition or still technology "in-progress" ?
What are your general opinions? How about sequencing COVID ?
I would appreciate any responses from the users :)
There is no comparison among sequencing technologies without specifying the purpose.
> main limitation of nanopore - bad accuracy
> How about support >> what support do you need?, applications available (are apps easy to use and free of charge ?) >> ease of using depends on the user and price of software would depend on what software you are using.
> The cost should be calculated from start to end of the project. However, if just sequencing cost is concerned, nanopore is relatively cheaper.
> nanopore technology is sure "in-progress"
> on general opinion with a proper aim/purpose.
> No one can sequence COVID on any sequencing technology at present or in future. Sequence its pathogen instead.
It's very hard to get wet lab nanopore going. Illumina is much more standardized and for majority of standard applications it is a very good choice. For something really in need of long-read sequencing I would suggest using Certified Service Prodivder. You can then consult your whole experiment with the scientific team and let them handle specialized applications in lab.
For Illumina there exist tons of free complete pipelines (look at nextflow pipelines). Nontheless investing in NGS without investing in experienced bioinfo team has short legs and you will never use the equipment to its fullest extent.
Thank you all for your replies. In my question, I assumed that the lab personnel is quite experienced in bioinformatics and has something to do with sequencing in general.
Abhijeet Singh As I mentioned, I have experience in Illumina technology, and I can support a new lab in that, however, some people ask me about nanopore, and I had nothing to do with that technology. I'm just curious if the nanopore sequencing is "complete" or as you said, still in progress. Of course what I meant was pathogen sequencing. Especially detecting SNVs and genome assembly.
Ireneusz Stolarek thanks, what do you mean that it's hard to get wet lab going? In what way it's more difficult or complicated comparing to e.g. Illumina ?
Nanopore had a good performance in short sequences in a few contings like a virus, but not in bacterial for example, and Ilumina can be best accuracy in the second one, but in many contings.
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