Is there any plant-specific genome assembler?

Question

[bioinformatics_bel]

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

[GenoMax]

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.

[Buffo]

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 :).

Answer 1

[Rayan Chikhi]

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

Answer 2

[Medhat]

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