I have some alignments of NGS data to the chicken genome which I used the NCBI assembly file to do. Now I'm trying to do some downstream analyses and we've decided to use the Ensembl annotation. I really don't want to have to rerun the alignments, since they took a few days to process, but the issue is that the names for the scaffolds in the alignments don't match the scaffold names in the annotation. Is there a mapping between the NCBI and Ensembl scaffold names somewhere? Is there an easy way to deal with this?