I have assembled four bacterial genomes derived from MiSeq pair-ended sequencing data using the following steps:
1 - Assembly using CLC Workbench;
2 - Assembly using SPADES;
3 - Assembly using A5 pipeline;
4 - Merging of the three assembles using CISA;
5 - Quality check of the assemblies using QUAST.
For checking the misassemblies, QUAST relies on a reference genome. However, for most of my draft genomes, I do not have a proper reference genome (too much genome differences in relation to those deposited in Genbank).
So, I ask you. How could I validate the genome assembly using intrinsic data? For example, using read mapping, what are the criteria to correct some regions? What is the best software for this purpose?