Homework_3

[tjcamp]

1. The N50 and L50 for both assemblies and state what these values mean: a. N50 - Canu = 4631892
   Spades = 133353 b. L50 - Canu = 1 Spades = 13

• N50 is the length for which the set of all contigs of that length or longer covers at least half (50%) the total base content of the Assembly. It serves as a median value for assessing whether the Assembly is balanced towards longer contigs (higher N50) or shorter contigs (lower N50). Larger N50 values can be indicative of better assembly.
• L50 is the number of contigs equal to or longer than the N50 length. In other words, L50, is the minimal number of contigs that contain half the total base content of the Assembly.

[tjcamp]

2. Upload .pngs of mummerplots for both assemblies and describe what these plots show:

• The mummer plots allow us to visualise the alignment of our sequence (query sequence on y axis) genome assembly with the reference genome (on x axis).
• In our case, image 1 (canu) shows the red color line which indicates that it has a substantial alignment with the reference genome. However, the location at which the query sequence aligns with the reference genome does not start at the zero point, and the alignment starts after the 1000000 mark.
• Image 2 (spades) shows the red color indicates that it has a substantial full-length alignment with the reference genome. (this can be inferred with respect to the color scale on the right side of the plot)

[tjcamp]

3. The URL to the location of the script on GitHub

   • https://github.com/tjcamp/BINF8940/blob/main/Homework_3.sh

4. The git revision used for your final analysis

   • 2472ff43ce35b58ef95fcc4476b3f001962e41a4

[JingxuanChen7]

1. Correct
2. Correct
3. Correct
4. Correct

@tjcamp Perfect job! Let me know if you have any other questions or concerns.