This is the repository to store codes and commands for the maize NC358 assembly and analyses. Please refer to different folders for different steps of the analyses, including:

1. Read depth downsampling and read length shifting
2. Genome Assembly
3. Gap fixing
4. Polishing
5. Super-scaffolding
6. Generation of pseudomolecules
7. Gene annotation
8. LTR_analysis
9. Assessing component assemblies
10. Figure plotting

Scripts in this repository are licensed under General Public License v3.

For information inquiry please email R. Kelly Dawe (kdawe@uga.edu), Candice N. Hirsch (cnhirsch@umn.edu), Matthew B. Hufford (mhufford@iastate.edu), or Doreen Ware (ware@cshl.edu).