I have done WES for various vertebrate species and have obtained contigs after running velveth and velvetg with various hashes and obtained good N50 values. My question now is, if I want to try assembling the contigs into a genome without using a reference, what tool is available for that for non-mammalian vertebrates? I want to be able to annotate all the assembled genomes afterwards to extract all protein-coding genes - can this step simply be done without having to do anything further with the contigs (i.e. can I use the contigs.fa files produced by velvet straight into annotation?)
I would also try the process where I do map the contigs using a reference genome using bwa mem but I want to implement both methods to see how the results vary.