This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Is there any plant-specific genome assembler?

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

plant assembly pine birch
• 2,806 views • link
updated by Medhat Medhat • written by bioinformatics_bel • bioinformatics_bel

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.

• 0 views • link
written by GenoMax GenoMax

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 :).

• 0 views • link
written by Buffo Buffo

2 answers

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

• 0 views • link
written by Rayan Chikhi Rayan Chikhi

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

• 0 views • link
written by Medhat Medhat

Log in to answer this question.

More posts like this