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README.md

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DOI

Raw reads have been submitted to Short Read Archive (SRA) as BioProject PRJNA612548 (SRA accession SAMN14377002).

Extended methods and results for baseline testing are found in

  • 01 Reference Construction.html (Reference_Construction.Rmd): Contains code and parameters used for de novo reference construction.
  • 02 Genotyping.html (Genotyping.Rmd): Contains details for read mapping, SNP calling, VCF filtering, and haplotyping of genomic data set used for analysis (data/POPGEN/CLE_by_est_genepop.gen)
  • scr/QDFA_script.R and scr/M_ANOVA_script contain reproducible code for analyzing microchemistry data (data/POPGEN/Cleucas_cemistry_data.csv)
  • TinHan_et_al2019_SuppMat.html (TinHan_et_al2019_SuppMat.Rmd) contains extended methods & results (including fully reproducible code) for baseline testing of genomic and microchemistry data.