I would like to compare three WGS datasets to each other, without using a reference genome. I am planning on running each set of paired end fastqs through SPAdes independently and then comparing the spades.contig files to each other.
I don't know of an alignment tool that doesn't require a reference genome as an input. I essentially want each of these files to be a reference to each other. I am also hoping for some kind of output that states the % aligned, similar to bowtie2.
I'm also looking for a tool that can do this, any luck finding it yet?
mummerto align the genomes in an all-vs-all pairwise manner. You can compute statistics on the alignments easily enough, but they will probably give you some already.
What is the expected size of the genome? Besides the tools mentioned by @Joe, you may need to look at LASTZ if these are eukaryotic genomes.
I think, Quast work for you. All you need to do is to check the parameters. It has got alignment parameter.