I have sequences from soil plantation sample. I already performed the assembly for my sequences using MEGAHIT but the result for N50 is too short, it's only around 500 bp. I have reed some paper that N50 is not only the parameter to say that our assembly is good, but i want to try my best to get good N50 for my data. I also already use another parameter of MEGAHIT to perform the assembly such as
--presets meta-large and
--min-count 1 but the result seem not really good. Do you have an advice for me to perform MEGAHIT to get a good assembly result? Or do you have other assembler recommendation to perform de novo assembly for shotgun metagenome from soil plantation sample?
Thank you so much for your help.