Question: Hybrid assembly using MinION data + correction with Illumina. Which strategy to adopt ?
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gravatar for lagartija
6 months ago by
lagartija10
lagartija10 wrote:

Hi there,

I want to assemble a bacterial genome using canu for the Minion data and correcting it with Illumina reads (I will also try to compare it to a hybrid assembler like SPades) but I do not know which strategy to use. As I understood well there are several ways to proceed : - Assembling with canu and then correcting the errors with a hybrid polish like pilon - Correcting the reads from Minion with Illumina with NaS for example and then assebling the genome

Which method would be the best ? I would prefere the first method because canu is already thought to correct the errors but I am not sure as our coverage from the Illumina data is better.

Thank you very much for your help, Cheers, Sofia

assembly • 498 views
ADD COMMENTlink modified 6 months ago by Rayan Chikhi1.4k • written 6 months ago by lagartija10

Try all of them. In my experience there isn't one method that just works all the time. Sometimes my Spades is better than my Canu. Sometimes my miniasm is better than my Spades,etc.

ADD REPLYlink written 6 months ago by Damian Kao15k

Thanks ! You are right, I will try both. Here I found a good comparaison https://pdfs.semanticscholar.org/ee7d/0333bf46248497ecdf2d9141903e5501e3d3.pdf

And another question, I don't really get the difference between SPades and HybridSPades as Spades. Isn't HybridSPades an algorithm implemented in Spades ?

Cheers,

ADD REPLYlink modified 6 months ago • written 6 months ago by lagartija10
0
gravatar for Rayan Chikhi
6 months ago by
Rayan Chikhi1.4k
France, Lille, CNRS
Rayan Chikhi1.4k wrote:

Have a look at https://github.com/rrwick/Unicycler

ADD COMMENTlink written 6 months ago by Rayan Chikhi1.4k
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