Project title: chromosome assembly and neo-sex chromosome of monk parakeet

This repository contains scripts that were used to produce genome assembly of a female monk parakeet (Myiopsitta monachus), including contig assembly the Hi-C based chromosome assembly. We also included scripts for genome annotations and other analyses. See details in each folder.

To generate the pair-wise alignment figure using MCScan, please see the script nucmer_to_mcscan.sh.

The code to generate Z-W sequence similarity in windows can be found here: https://github.com/lurebgi/BOPsexChr