Question: Is there any plant-specific genome assembler?
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gravatar for bioinformatics_bel
7 weeks 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 • 232 views
ADD COMMENTlink modified 7 weeks ago by Medhat7.3k • written 7 weeks 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 7 weeks ago • written 7 weeks ago by genomax40k
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 7 weeks ago by Buffo590
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gravatar for Rayan Chikhi
7 weeks ago by
Rayan Chikhi1.2k
France, Lille, CNRS
Rayan Chikhi1.2k 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 7 weeks ago • written 7 weeks ago by Rayan Chikhi1.2k
0
gravatar for Medhat
7 weeks ago by
Medhat7.3k
Poland
Medhat7.3k 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 7 weeks ago • written 7 weeks ago by Medhat7.3k
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