Farhat Laboratory's repositories
gentb-site
The genTB project, the Django site, variant calling and prediciton pipeline, and mapping pipeline with hooks to two ravens
mtb-illumina-wgs-evaluation
Repository for analysis of Benchmarking the accuracy of short-read sequencing across the M. tuberculosis genome, 2022, Bioinformatics.
resdata-ng
DB of MTB resistance data and isolate metadata
metatools_ncbi
Download biosample and SRA runinfo metadata from NCBI
who-analysis
Code used for WHO analysis work
GenotypeTools
Python code for reading, writing, and analyzing genotypes in various file formats
gentb-snakemake
From FASTQ file to antibiotic resistance prediction using RandomForest - the GenTB pipeline wrapped in snakemake
phase-variation-in-Mtbc
Jupyter Notebooks used in data analysis for "Phase variation as a major mechanism of adaptation in Mycobacterium tuberculosis complex" (Vargas et al. 2023)
AISC610_darwinian_medicine
Practical exercises for the Darwinian Medicine class of the AISC610 course
analysis_pipeline
Pipeline that takes user country-lineage-drug queries and output SNP alignment/BEAST tree output
epistasis-KAN-BDQ-Mtbc-resistance
Jupyter Notebooks used in data analysis for "The role of epistasis in amikacin, kanamycin, bedaquiline, and clofazimine resistance in Mycobacterium tuberculosis complex" (Vargas et al. 2021)
EVcouplings
Evolutionary couplings from protein and RNA sequence alignments
geo_dist_tb
Place to store code used for manuscript
in-host-Mtbc-dynamics
Jupyter Notebooks used in data analysis for "In-host population dynamics of Mycobacterium tuberculosis complex during active disease" (Vargas et al. 2021)
mtb-pg-benchmarking-2024paper
All code for data processing and analysis described in "Analysis of the limited M. tuberculosis pangenome reveals potential pitfalls of pan-genome analysis approaches" (Marin-2024)
Non-tuberculous-Mycobacteria-Chart-Review
Variable extraction for partners health system .txt file format database to dataframe for analysis in python or R.
peru_cluster
Code used for analysis of Peru cluster