This is the analysis pipeline for ctyper. The code here is for the record of reproducibility. However, due to the workload, we cannot provide maintenance for the code in this repository. If you interested in using some of idea or methods include here in your own projects, please email us at wangfeim@usc.edu and mchaisso@usc.edu.

Some of code relies on intermediate results from prior analysis, which can be found at https://zenodo.org/records/13683015. Some others could be too big or too many files to all includes. Those data could be regenerated or accessed via requested from wangfeim@usc.edu and mchaisso@usc.edu.

The under maintained ctyper genotyping tool can be found at: https://github.com/ChaissonLab/Ctyper