Skip to content

Latest commit

 

History

History
25 lines (21 loc) · 1.44 KB

README.md

File metadata and controls

25 lines (21 loc) · 1.44 KB
Raw

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.