Gathering information for programs and assemblers used for DNA de novo assembly with long reads. Hoping to publish a libguide to help students around our campus. If you have done de novo assembly with long reads, what is your favorite assembler you used and why? What was the sequencing company you used? What organism type were you working with (plants, bacteria, mammalian, etc.)? What other programs did you use that helped while processing these reads (overlap detection, polishing, scaffolding, etc.)? Any and all information is appreciated!
I have found many programs and assemblers while researching this, but since I have personally never done de novo assembly with long reads, I am hoping to get input from those that have.