Homework_3

[jcu23686]

1.)
ecoli.contigs N50 4631892 L50 1
scaffolds N50 133353 L50 13

N50 is the contig for which 50% of the assembly is covered
L50 is the number of contigs in which 50% of the assembly is covered

In ecoli.contigs it took 4631892 Mb to assemble 50% of the genome
In scaffolds it took 4631892 Mb to assemble 50% of the genome

In ecoli.contigs it took 1 contig to assemble 50% of the genome
In scaffolds it took 13 contig to assemble 50% of the genome

2.)
Canu

spades

The lines appear to be fairly straight for each plot so we know that contigs must have aligned fairly well. In the spades plot there is some discontinuity as some dots are not along the diagonal line.

3.)
https://github.com/jcu23686/BINF8940/blob/main/homework3.sh
4.)
e4ce210

[JingxuanChen7]

1. Correct
2. Good job in generating the dot plots. Small points to add in explaining the plots: The canu png shows assembly of a single circular contig that is perfectly colinear and very similar in sequence to the reference genome, but appears offset because it starts at a different first base than the reference genome.
3. Correct
4. Correct

@jcu23686 Great job! Let me know if you have any other questions or concerns.