This repository hosts codes and results for pairwise whole genome comparison between any two genome (moslty maize) assemblies.
- minimap2 was used to align one assembly to another;
- blat chain/net tools were used to process alignment resuls and build synteny chains/nets;
- bcftools and GATK4 were used to call variants;
- snpEff was used to evaluate variant effects on sytenic genes
See this page for a sumamry of comparing four maize de novo assemblies (W22, Mo17, PH207 and PHB47) to the B73 reference.