Frequently Asked Questions

Does XYalign require X and Y chromosomes?

In principle, no, it doesn’t. The focus on X and Y chromosomes stems from our initial interest in characterizing technical biases and aneuploidies affecting variant calling on the sex chromosomes in large human genomic datasets. Hence, the terminology we use throughout. You can provide the name of any chromosome or scaffold to --x_chromosome and --y_chromosome, and an arbitrary number of chromosome/scaffold names to --chromosomes. See Usage Overview for an example of how this might work. We plan to generalize XYalign in the future to make this easier.

Will XYalign work with genomes from other organisms?

Yes, but with some caveats. As discussed above, you can provide any chromosome names to --x_chromosome and --y_chromosome. So, if your organism has Z and W chromosomes, this might look like --x_chromosome chrZ and --y_chromosome chrW. However, we advise users to interpret results cautiously, as XYalign’s default settings for human X and Y chromosomes are likely inappropriate for many other organisms. This is especially the case for ZW systems, or reference genomes without sequences for the Y (or equivalent) chromosome. In addition, XYalign does not currently accept multiple X or Y scaffolds. We plan to address these phenomena in future releases.