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Leia01 09-11-2019 06:25 PM

Determining quality of genome assembly
 
Hi! I apologize for this really basic question, as I am new to the field.

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

I understand that quality is a relative term and that there are several options for assessing genome assemblies (QUAST, BUSCO, etc.) but I am not confident on how to use those tools. I am at a loss of where to start, so any information will be greatly appreciated!


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