Hi, I was wondering if someone knew how to analyze the quality of an assembly. I used bandage info and the result was a table with different statistics, like node lenght, dead ends… I know what each of the metrics mean however i do not know how to determine wether the results were of good quality or not.
Hello!
What type of assembly did you perform, i.e., is this a de novo assembly for one individual, or a metagenomic project?
Speaking for the de novo assembly case – “good quality” is relative, but you can get an idea of how fragmented your graph is by looking at percentage dead ends
. For instance, this is a graph with ~16% dead ends:
And this is a graph with ~4% dead ends:
(I know the images are really faint try opening in a different tab)
That being said, I usually find it more helpful to look at the output of the Bandage Image
tool to get a drawing of your assembly graph, instead! Looking at the graph visually helps me understand my results more than the table of stats, typically. Here is the tool: Galaxy
REF: Learn at GTN → Hands-on: Unicycler Assembly / Assembly