I'm looking for pipeline recommendations. I have DNA sequencing data by pacbio (15G) coming from a plant with a genome of approximately 3G. I want to perform de novo assembly and guided assembly (if it could be possible) and I would like to know what options you recommend to perform a guided assembly of a reference, since I have a genome very close to the species I want to assemble.
Here is a recent review about assembling complex plant genomes. Hard to give suggestions as there is no indication of the complexity of the genome including repetitive element composition and ploidy. But you could use assemblers that include phase information from long reads like HiFiasm or Canu.
I would suggest starting with a de novo contig assembly, and then you can use tools like RagTag to use a reference to scaffold your assembly if necessary. Starting with raw reads and using reference to guide assembly is not a good way to start an assembly. You inherit all of the misassembles and may incorrectly orient and order reads due to fixed differences among assemblies. But generally, I would suggest avoiding reference-guided approaches unless they are strains/ecotypes/subspecies of the same species, and even then to be wary.
you can have a look at https://link.springer.com/article/10.1007/s12223-022-00980-7 but i do not know If it works for you.