Code for "Reducing mapping reference and lineage bias in Mycobacterium tuberculosis"

1. Simulations and variant calling:

ART Illumina simulations: 1_art_sims.sh
Mapping only pipeline: 2_mapping.sh
Hybrid mapping and assembly pipeline: 3_assembly_mapping.sh

2. Analysis of bias

VCF comparison: 4_compareVCfs.R
Build null distribution: 5_null_dist.R
Infer error model: 6_errorModel.R
Calculate and plot bias: 7_mappingBias.R