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 + misassemblies

Q8. Contaminations + misassemblies

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 a lot of the reference genome is covered by our assembly, so yes.

Q11. very few and the K119.81 only maps partially. This could be a sequence in our strain, but not in the reference genome. Or a misassembly.

Q12. This is a region with a lot of repeats, this is also why we can't really assemble it. It is used by V. cholerae to integrate new genes into its genome.

Q13. Using:

 
grep ">" ecoli_nanopore.contigs.fasta
grep ">" ecoli_pacbio.contigs.fasta

The Nanopore assembly only has 2 contigs and pacbio 1! Pretty good!

Q14. using:

/home/ctools/prokka/binaries/linux/prodigal -f gff -i ecoli_pacbio.contigs.fasta -a ecoli_pacbio.contigs.aa -o ecoli_pacbio.contigs.gff

it is the Beta-galactosidase gene of E.Coli. That gene was used by François Jacob, André Lwoff and Jacques Monod to describe gene regulation in 1960 which got them the Nobel prize in 1965