I am dealing with shotgun metageomincs data with 100bp paired-end reads from Hiseq.
I have used the default setting in metaSPAdes, IDBA and MEGAHIT to assemble the reads. But I do not know which one is better. Any suggestions? Are there any indicators to evaluate it? Even I know some software like QUAST can do this, they give me too many parameters, I do not know to choose which one. May I know %raw reads can be assembled matters? How to know how many reads can be assembled?
Thanks in advance.