Hybrid Assembly Strategies (smaller/prokaryotic genomes)

Hybrid Assembly Strategies (larger/eukaryotic genomes)

Note that these were suggestions for an algal assembly from Dr. Chris Fields and Kim Walden at UIUC's bioinformatics core, HPCBio.

Get a good estimate of the genome size using your illumina reads and Genome Scope. You will need to get a kmer histogram from your illumina data to use as input to Genome Scope, and you can use KMC or Jellyfish for that.
Workflow
- Assemble Nanopore reads using something like wtdbg2, Flye, or miniasm (might need to use multiple assemblers and test which works best)
- Do a first round of assembly polishing with nanopolish, using only nanopore data
- Do a second round of assembly polishing with Racon or Pilon, using illumina data this time
Use BUSCO for assessment
If your Nanopore data was generated using tech from before 2020 using older flow cells, you may have to re run the basecalling using something like Guppy (speedy if you can use GPUs)