BioinformaticsTools

Repo with pipelines and scripts I used frequently for bioinformatics analysis of my MSc project. Project entitled "Creating and analysing an African pan-genome".

Analyses included:

• PythonPlots: directory containing JupyterNotebooks for all the plots presented in my dissertation. Analyses included are (by order of appearance in the dissertation):

  • CD-HIT cut-off and contig length distribution plots in Plots.ipynb
  • alignment of 1kGP data to GRCh38 in 1kGPvb38.ipynb
  • PCA and upset plot for 1kGP data 1kGpca&upset.ipynb
  • MultiQC analysis plots in MultiQCplots.ipynb
  • contamination scatter plots in Plots.ipynb
  • population non-ref seq bar graphs in Plots.ipynb
  • repeat element stacked bar graph in Plots.ipynb
  • pan-African PCA and upset plots in PlotsAfricanPCA.ipynb and PlotsAfricanUpset.ipynb
  • MAKER genes upset plots in MAKERgeneUpset.ipynb
  • all alignment plots in PlotsAlignment.ipynb
  • analysis of core and distributed genes at different cut offs in PAVanalysis.ipynb
  • core genes plots in Plots.ipynb
  • PAV profiles in Plots.ipynb

• QuastMultiQC: directory containing the MultiQC reports for the starting dataset and final dataset for the African pan-genome, and the Nextflow pipeline config files used to create those reports.

• alignment: directory containing the Python script used to analyse all alignment outputs from NUCmer and pblat.