This repository documents the analyses of the leading to the illustration of the somatic genome landscapes of Marek's Disease (MD) Lymphomas.

This repository should be referenced in accordance with Hongen Xu's comprehensive repository at https://github.com/hongenxu/MDV_proj.

There are 5 primary folders:

• 00_genomic_datasets (primary code from Alec):
  • The collection and curation of additional genomic datasets.
• 01_reference_prep (primary code from Hongen):
  • The collection and curation of the Galgal 5.0 reference genome
• 02_fastq_to_bam (code from both Alec and Hongen--replicate analyses):
  • The processing pipeline from investigation of raw reads to mapping reads on the Galgal5 genome
• 03_germline_snvs_indels (primary code from Alec):
  • The detection and filteration of germline snvs and indels
• 04_somatic_snvs_indels (primary code from Hongen):
  • The detection and filteration of somatic snvs and indels in MD tumors.