Denovo solution

Q1. Illumina

Q1A. discarded contains reads that are too short, pair1 and pair2 files contain the read pairs were both passed trimming and singleton are reads were one of the two pairs were discarded.

Q2. Around 84

Q3. N = (M*L)/(L-K+1) = (84*99)/(99-15+1) = 97.84 Genome_size = T/N = (213721367+212523694)/97.84 = 4.35Mb

Q4. Mean = 259 ; SD = 11

Q5. It is higher N50:179846 than the best we found at k=79 N50:92020

Q6. 1

Q7. Repeat regions + missamblies

Q8. Contaminations + missamblies

Q9. Because we use the reference genome as the truth it may be hard to distinguish what is a misassembly and what is true variation from the reference genome.

Q10. This is just visual, but it seems that most of the reference genome is covered by our assembly, so yes.

Q11. Yes, a couple of the small contigs does not map at all, and the C1097 only maps partially. This could be sequence in our strain, but not in the reference genome.

Q12. This is a region with a lot of repeats, this is also why we cant really assemble it. It is used by V. cholerae to integrate new genes into its genome.

Q13. The Nanopore assembly only has 2 contigs and pacbio 1!