The MTb-ISEMapper pipeline analyzes paired-end short-read WGS data for M. tuberculosis isolates.
At a high-level the pipeline has the following steps:
- Subset the input data for reads that align to the IS6110 reference sequence. (IS6110 reads)
- Align the IS6110 reads to the H37Rv genome. Note this version of the H37Rv genome must have all IS6110 elements masked.
- Calculate alignment depth for IS6110 reads across the H37Rv genome.
- Analyze depth to identify putative IS6110 insertion locations.