ash-bell / masters_thesis Public

GitHub Repo for all the scripts used in my Master's Thesis

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Name		Name	Last commit message	Last commit date
Latest commit History 36 Commits
Ashley Masters 6 Month review.docx		Ashley Masters 6 Month review.docx
Ashley Masters 6 month review.docx		Ashley Masters 6 month review.docx
Ashley Masters Thesis (ROUGH).docx		Ashley Masters Thesis (ROUGH).docx
Ashley Masters Thesis.docx		Ashley Masters Thesis.docx
Gannet chart.drawio		Gannet chart.drawio
Long reads assembly.drawio		Long reads assembly.drawio
Metagenomics Method.drawio		Metagenomics Method.drawio
PIC Extraction Method_BIOS.doc		PIC Extraction Method_BIOS.doc
Phylogenetics method		Phylogenetics method
QC_reads.smk		QC_reads.smk
README.md		README.md
THESIS_BACKUP_23_06_20.zip		THESIS_BACKUP_23_06_20.zip
ani_plot.py		ani_plot.py
anvio.sh		anvio.sh
barplot_relative_abundance.py		barplot_relative_abundance.py
checkm.sh		checkm.sh
extract_HVR.sh		extract_HVR.sh
fastANI.sh		fastANI.sh
fastANI_heatmap.png		fastANI_heatmap.png
fastANI_heatmap_no_structure.xcf		fastANI_heatmap_no_structure.xcf
gene_annotation_viral_signatures.sh		gene_annotation_viral_signatures.sh
genome_visualisation.py		genome_visualisation.py
hype_geom_test.py		hype_geom_test.py
kmer_freq.py		kmer_freq.py
kmer_plot_100k_genome_frag.sh		kmer_plot_100k_genome_frag.sh
mapping_95pc.sh		mapping_95pc.sh
plot_bin.py		plot_bin.py
plot_kmer_bins.py		plot_kmer_bins.py
prokka.sh		prokka.sh
ridgeline_plot.py		ridgeline_plot.py
run_hdbscan.py		run_hdbscan.py
run_umap.py		run_umap.py
single_cell_assem.sh		single_cell_assem.sh
violin_plot_scaffold_cov.py		violin_plot_scaffold_cov.py
virsorter.sh		virsorter.sh