What tools are proper for plant genome pre- and post-assembly and annotation of the de novo results?

Question

[bioinformatics_bel]

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.

Answer 1

[Sergey Naumenko]

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

Answer 2

[colindaven]

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 ($$$$).