Discussion prompts for long read sequencing overview papers - mestato/EPP622_2026 GitHub Wiki

1. Check understanding - how do long reads differ from short reads?

   • read length
   • cost (you may need to look this up outside of the papers)
   • sample input requirements
   • output quality
   • companies
   • chemistry

2. For each of these research use cases, why are long reads better?

   • genome assembly
   • structural variant analysis and/or repetitive element analysis
   • methylation analysis
   • haplotype phasing (wondering what phasing is? See this image from pacbio website below)

3. Reference-based mapping vs. de novo assembly. The Hitchhiker's Guide frames this as the first critical fork in the workflow (Fig. 2). What is the difference and how would you pick which to use for a given project?

4. Mahmoud Table 1 lists 70+ tools, and several key ones are cited only as preprints. Despite only being 3 years old, some of these tools are no longer in widespread use while many others have emerged. How do you choose tools in a field moving this fast?

5. "Sequencing toothbrush" - going to happen one day or not? If so, how far in the future?

Phasing