Dear all, I have Illumina fastq reads of small eukaryotic genome (Chlamydomonas sp.). I am doing its genome assembly using Spades (de novo assembler) and after this I want to structurally and functionally annotate the genome. Before moving to annotation part, I should know the quality of the assembled genome. For this, I have run Quast and got L50, N50, GC content etc. I want to know if my N50, L50 is good or I should assemble the genome with other assemblers. I know that N50 must be high but how much high is the question? Is there a cut off for N50 or L50? Overall I want to know if my assembly is ready for annotation or it need other steps to be done and if it needs to improve, how can I improve a genome assembly?
Thanks in advance