.Did the genome assembly you performed guarantee the optimal assembly? Explain why or why not. (Rhodobacter spheroides genome and assembled with SPAdes)
2. What sequencing libraries would you suggest adding, and what assembler would you recommend to improve the N50 of the Rhodobacter genome? Explain how the additional libraries would help.
3. Describe the purpose and approach to a metagenome assembly.
4. What characteristic of many genomes violates one of the underlying assumptions behind genome assembly algorithms?
5. Which type of assembler (de Bruijn graph or OLC) do you think would be more appropriate for PacBio data?
6. What would you suggest including as part of the sequencing strategy for a genome with many repeat regions? Why?
7. What procedure was a typical way of finding genes prior to the development of gene-start prediction models?
8. ALLPATHS produced a higher N50 than any other assembler in the original GAGE study, so why might a lab choose the MaSuRCA or SPAdes assembler for a bacterial genome project?