Hi there,
Here I have a question related to phage DNA sequencing work. We have several phage species isolated from sewage and we need to sequence their DNA. The method available here is the Illumina HiSeq or Illumina MiSeq. These methods are pretty powerful but are too expensive for us.
Is there any other good methods for sequencing the phage DNA (whole genomic DNA) with low cost? For the Illumina sequencing method, each time we need to purchase one lane and the cost is around 2000 dollars (including the fee for DNA library preparation and some other work).
Thanks a lot!
Dear Chiqian,
We have sequenced phage genomes on almost all platforms. Roche 454 and Illumina MiSeq are both giving very good results, but are as you write expensive if you run single samples. We have pooled up to 20 genomes in a lane, which brings down the cost per genome a lot. For single genomes however it is better to use the PacBioII system. The error rate is quite high (15%), but the coverage is in the thousands for an average sized phage genome, and the cost per genome around $650.
/Anders
Dear Chiquian,
I have sequenced phages with less than 300 dollars per sample using illumina Hi seq for 100mb of clean data in a private company including library construction so asking you 2.000 dollars is way too much. Maybe you have asked also for bioinformatics work (quality trim, assembling, annotations etc etc) and thats why the cost is that much (which in my opinion is again very high).
Dimitris
Dear Chiquian,
I have sequenced phages with less than 300 dollars per sample using illumina Hi seq for 100mb of clean data in a private company including library construction so asking you 2.000 dollars is way too much. Maybe you have asked also for bioinformatics work (quality trim, assembling, annotations etc etc) and thats why the cost is that much (which in my opinion is again very high).
Dimitris
Cost-effective way for phage DNA sequencing?. Available from: https://www.researchgate.net/post/Cost-effective_way_for_phage_DNA_sequencing#view=553a5629d11b8b39338b4695 [accessed Apr 24, 2015].
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Dear Dimitris,
Thank yo so much for the information! Your price sounds very good. Here we are using the service of our university's DNA Center. The 2,000 dollars includes the preparation of the DNA library but does not include the bioinformatics analysis, The service for the bioinformatics is charged separately.
Another reason why our price is expensive is that no matter how many phages you have, you need to purchase one lane. If we can find someone who needs phage sequencing as well, we can share the lane and reduce the cost. However, we did not find another group around us doing the same thing at thia point.
So, may I know the name of the private company that you used for phage sequencing? Also, are they mix your samples with the ones from other costumers so that the price can be cut?
Once again, thank you so much for the answer!
Yours,
Chiqian
Dear Chiqian,
We have sequenced phage genomes on almost all platforms. Roche 454 and Illumina MiSeq are both giving very good results, but are as you write expensive if you run single samples. We have pooled up to 20 genomes in a lane, which brings down the cost per genome a lot. For single genomes however it is better to use the PacBioII system. The error rate is quite high (15%), but the coverage is in the thousands for an average sized phage genome, and the cost per genome around $650.
/Anders
Cost-effective way for phage DNA sequencing?. Available from: https://www.researchgate.net/post/Cost-effective_way_for_phage_DNA_sequencing#553a6cd9ef97135d238b45a8 [accessed Apr 24, 2015].
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Dear Anders,
Thank you so much for the answer. That helps. Based on your experience, I think we might need to stick to the Illumina method as the other method you mentioned has quite high error rate and is not available here.
Thanks again!
Yours,
Chiqian
Beijing Genomics Institute. You should be able to google it and get a contact email to get more information and see from there if suits for you or not.
Cheers,
Dimitris
I see. Thanks a lot. I come from China and know this company. I will contact them. Did you send your DNA samples oversea for the sequencing?
I used courier which they made the transport via plane in 3 days. Ice packs where more than enough for transport assuming you had superb DNA quality with only small degradation. Talk to them, they will be very helpful to guide you through the process.
Cheers,
Dimitris
Thanks you so much, sir. I will contact them and discuss it. Good information!
Dear Chiqian,
I lead a Roche reference sequencing laboratory. We use Roche 454 Junior+ (producing 700 bp long reads) for phage DNA sequencing. If you have phages with a genome size of 100 kb, you can load 10 samples and you will get a nice coverage enabling the assembly of the genomes. One such run costs approx. 1000 USD, i.e. 100 USD/sample.
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