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
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 ($$$$).