Question: Is there any plant-specific genome assembler?
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gravatar for bioinformatics_bel
12 months ago by
US, Alaska
bioinformatics_bel20 wrote:

Is there any plant-specific genome assembler? Need it for forestry: birch and pine genome data processing. Thx.

pine assembly plant birch • 532 views
ADD COMMENTlink modified 12 months ago by Medhat8.0k • written 12 months ago by bioinformatics_bel20
2

Are ploidy considerations the reason for this question? Hexploid bread wheat genome was recently assembled with two aligners and two types of data. Rather than a specific aligner, having long read good quality data along with short read data (and a ton of both) seems to be the secret of sauce required for complex genomes.

ADD REPLYlink modified 12 months ago • written 12 months ago by genomax59k
1

You will need a powerful machine (specially RAM memory) more than special assembler, at least pine genome are expected to be in the order of 20 Gb :).

ADD REPLYlink written 12 months ago by Buffo1.2k
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gravatar for Rayan Chikhi
12 months ago by
Rayan Chikhi1.4k
France, Lille, CNRS
Rayan Chikhi1.4k wrote:

I'll mention this one, that is a fork of Discovar that was used to assemble a wheat: https://github.com/bioinfologics/w2rap-contigger

ADD COMMENTlink modified 12 months ago • written 12 months ago by Rayan Chikhi1.4k
0
gravatar for Medhat
12 months ago by
Medhat8.0k
Poland
Medhat8.0k wrote:

Yes there is Platanus. In case of highly repetitive genome It would be better if you could incorporate long reads (PacBio, nanopore, 10X genomics). In this case you will change your strategy of assembly

here is a nice paper that may help you The impact of third generation genomic technologies on plant genome assembly

ADD COMMENTlink modified 12 months ago • written 12 months ago by Medhat8.0k
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