This repository contains code supporting analyses presented in Hernandez et al. Specifically, we provide the code used for:
- running RepeatMasker on the genome and indexing both the masked genome and mitogenome in 1_RepeatMask
- Quality control of paired-end libraries for the PSMC and genome-wide heterozygosity in 2_QAQC. The same workflow was run for both individuals, so we present the scripts and corresponding text files for z0045928.
- Code to run the PSMC and genome-wide heterozygosity analyses in 3_Analyses
Note that these scripts were run on NOAA's Sedna bioinformatics cluster, and can be adapted based on one's available computing resources.
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