Question: What tools are proper for plant genome pre- and post-assembly and annotation of the de novo results?
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gravatar for bioinformatics_bel
22 months ago by
US, Alaska
bioinformatics_bel20 wrote:

What tools are proper for plant genome pre- and post-assembly and annotation of the de novo results? Need specific tools for pine and birch genomes or some universal software, if possible.

ADD COMMENTlink modified 22 months ago by colindaven1.7k • written 22 months ago by bioinformatics_bel20
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gravatar for Sergey Naumenko
22 months ago by
Sergey Naumenko350 wrote:

Hi bioinformatics_bel!

What a brave researchers you are to work with those huge genomes! I'm afraid there is no pine- or birch- specific tools, or any universal software for that genome size. I hope you are aware of the Norway spruce genome project (https://www.nature.com/articles/nature12211) and pine genome (https://genomebiology.biomedcentral.com/articles/10.1186/gb-2014-15-3-r59). Try to study their methods and apply them!

I think, the key points will be

  • having libraries of different insert sizes (planning your sequencing well ahead)
  • figuring out, whether you can do reference guided assembly (depends on the similarity of your genome and of another pine that was published) or should you go for de-novo
  • having access to a computer node with huge RAM (1-3T).
  • sequencing transcriptome to help with annotation.
  • combining assemblers and scaffolders developed for genomes of smaller size, say velvet (https://www.ebi.ac.uk/~zerbino/velvet/) + platanus (http://platanus.bio.titech.ac.jp/?page_id=14) for a rough draft.

Those thoughts are quite obvious, I hope at least something was useful for you.

Good luck! SN

ADD COMMENTlink modified 22 months ago • written 22 months ago by Sergey Naumenko350
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gravatar for colindaven
22 months ago by
colindaven1.7k
Hannover Medical School
colindaven1.7k wrote:

Unless you're an expert on de novo assembly and have big memory clusters available, I'd go for a resequencing approach. The work behind genomes of this size is immense. Or collarborate with them.

If I was doing a genome of this size de novo, I would demand long reads ($$$$).

ADD COMMENTlink written 22 months ago by colindaven1.7k
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