This directory contains the source code for version 1.1.6 of XYalign, as well as all files used to assemble and analyze data for the updated preprint and initial XYalign publication. This work was supported by the National Institute of General Medical Sciences of the National Institutes of Health under Award Number R35GM124827 to Melissa A. Wilson Sayres. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

The high degree of similarity between gametologous sequences on the sex chromosomes can lead to the misalignment of sequencing reads and substantially affect variant calling. Here we present XYalign, a new tool that (1) quickly infers sex chromosome ploidy in NGS data, (2) remaps reads based on the inferred sex chromosome complement of the individual, and (3) outputs quality, depth, and allele-balance metrics across chromosomes.