I am using QUAST in Kbase to assess the quality of my genome assemblies of bacterial isolates.
The report from QUAST provided parameters such as N50 and Mismatches. I have found their meaning in https://quast.sourceforge.net/docs/manual.html#sec3.1. And I have learned that an ideal genome is contiguous, complete, and correct.
Most studies suggest the lower the mismatches or other values are, the better the quality will be.
However, are there any absolute values/thresholds that could be used to test whether this assembly is good quality?
(Some studies showed that the threshold depends on the size of the genome and the goal of the study. Then is there any way to calculate this threshold?)
Thank you very much!
No absolute thresholds. Genome assembly is still very manual work.
However, QUAST scores are very simplistic. You should invest time and explore other metrics if you care about good genome assembly.
You can start with recommendations https://www.biostars.org/p/47224/#335008 (definitely at least BUSCO, Reapr, KAT). A sort of alternative to KAT would be Merqury, which is also very popular https://github.com/marbl/merqury. I also quite like ideel https://github.com/mw55309/ideel as part of assembly QC. You can do a simple read mapping back to the assembly and look for the number of mapped reads, the percentage of properly paired reads, ... Good assembly is a lot of work any many back-and-forth iterations.
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