Here we introduce the pipeline for achieving haplotype-resolved, chromosome-level genome assembly of tetraploids using reference genome, long read sequencing and HiC sequencing.
Befrore running the pipeline, install necessary customized tools, check INSTALL.
To start the process, check the pipeline
Note, tools required are listed in the beginning of the pipeline. Please install following their instructions.
Here is also the pipeline for diversity and introgression analysis: Diversity_Introgression_Selection_Analyses.md