Determining the quality of a publicly available genome assembly I am looking for homologous genes in various protozoan species using BLAST. The genome sequences of these species are deposited in NCBI's WGS database. NCBI’s webpage includes the global statistics for each WGS project and it indicates the assembly level (scaffold, contig, etc.), the assembly statistics (number of contigs, N50, L50, etc) and (if available) the genome coverage. Can any / some of these parameters be used to evaluate the genome assembly’s "quality", especially if there is more than one genome assembly for the same species? Can these data be used to determine if the genome is very fragmented or not?

I understand that quality is a relative term and that there are several options for assessing genome assemblies (QUAST, BUSCO, etc.) but I am just looking for a "simple" way to compare several genome assemblies (for e.g., this post How can I improve a long-read assembly with a repetitive genome? states that the reference genome is highly fragmented, but there is no explanation regarding how the OP determined this). I believe that the N50 value can be helpful, but I need some context to understand what is "good" or "bad".  I am at a loss of where to start, so any information will be greatly appreciated! 

-Leah
It is not so easy to determine the quality of an assembly - but sequence length, number of contigs, N50 and L50 can give you some guidance.

How much does the sequence length deviate from the expected length (or how much variation is among assemblies of the same species). Same for number of contigs/scaffolds. The sequence length, and number of contigs together with N50 and L50 give you an idea about the fragmentation. Very small N50 compared to expected genome size and chromosomes is a likely indication of high fragmentation, same for high L50 compared to expected number of chromosomes.

However, these number can be misleading. High N50 and low L50 can occur witho some very long contigs, so you may want to compare N75/L75 or better the Quast statistics