Entering edit mode
7.9 years ago
agata88
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870
Hi all,
I need to design a project for whole genome sequencing of plant which size is around 150725 bp. I would like to use MiSeq sequencer.
I would appreciate for any suggestions for questions listed below:
Which kit would you recommend for such analysis?
How much coverage do I need to perform genome de novo assembly?
How much memory and disc space do I need to perform plant genome de novo assembly?
If I would send MiSeq results to other company for bioinformatic analysis, do you know how much it will cost me?
Thank you in advance,
Best,
Agata
You have a plant genome that's only 150kb? That would have to be some kind of record..
It is a plastid genome the most related to Spinacia oleracea.
Are you going to isolate the plastid DNA before making the library? That would make this project simple.
With such a small genome you could mix this library with some other pool (and not have to pay for a full MiSeq run) and still have plenty of reads. If there are no repeats etc you would need few resources to do the de novo assembly.
I think I will have only plastid DNA. There are repeats, in second part of analysis I need to find repeats and compare them to known. So, what kit would you recommend? And how much will it cost me in your opinion?
If the related reference is reasonably complete then you can leverage that information.
You should be able to use any standard DNA library kit (disclaimer: I don't work in the lab so you would want to verify with someone knowledgeable). You would still need to figure in cost of the kit but you can share the actual run cost with someone who has a larger pool to run and pay only the fractional cost for sequencing. If you are not going to make the library then add the cost for getting someone else to do it. AllSeq and Genohub are two NGS data provider aggregator sites. You can get an idea of how much the project may cost by visiting those sites.
Ok. Thank you very much :)