Universal functions and scripts for TB bioinformatics analysis pipelines

db - Database of useful tables - see also https://github.com/jodyphelan/tbdb/

• country_code_lookup.txt
• lineage_conversions.txt
• lineage_conversions_meta.md

python_scripts

• init.py
• cut_tree.py
• gwas.py
• run_fst_analysis.py
• tbprofiler_filter.py
• tree_functions.py
• utils.py

r_scripts

• babette.R
• beast_xml.R
• itol_annotation.R
• itol_templates.R
• nexus2nwk.R
• rscripts_template.R
• rvlookup
• transphylo.R
• transphylo_inferTTree.R

shell_scripts

• bash_aliases [from Julian]
• bash_functions [from Julian]
• generate_representative_tree.sh
• iqtree.sh
• merge_vcfs.sh
• multisample_median_cov.sh
• plink_dist_and_pca.sh
• subset_fasta.sh
• variant_calling_and_concat_gvcfs.sh
• variant_filtering.sh
• vcf2fasta.sh
• vlookup