Code associated with the manuscript "High short tandem repeat mutation recurrence in heat-stressed Arabidopsis thaliana lines" by William B. Reinar, Anne Greulich, Vilde O. Lalun, Melinka A. Butenko, and Kjetill Jakobsen.

This repository contains a Python Notebook with code ('arabidopsisGenerationAnalysisBashNotesSubsampling-Copy1.ipynb' used to map, align and perform initial variant calling and quality control of raw reads resulting from the mutation accumulation experiment. The raw reads are available from NCBI Short Read Archive accession: PRJEB70284.The repository also contains:Variant calls from HipSTR (raw and filtered) and GATK4.0.A Python Notebook ('Gen_Pipeline_and_Figures-Copy1.ipynb' with the code used to identify accumulated variants, do statistics and produce figures.<br>