Data and code for: In Vivo Evolution of an Emerging Zoonotic Bacterial Pathogen in an Immunocompromised Human Host
Creators
- 1. Bacterial Pathogenesis and Antimicrobial Resistance Unit, LCIM, NIAID, Bethesda, MD
- 2. Dept. Laboratory Medicine, NIH Clinical Center, Bethesda, MD
- 3. Bacterial Pathogenesis and Antimicrobial Resistance Unit, LCIM, NIAID, Bethesda, MD ; Dept. Laboratory Medicine, NIH Clinical Center, Bethesda, MD
Description
This repository contains code and the data for reproducing results and figures in the associated manuscript: "In Vivo Evolution of an Emerging Zoonotic Bacterial Pathogen in an Immunocompromised Human Host".
1_ancestor_reconstruction:
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Script and data to reproduce the reconstructed ancestor.
2_mutation_cleanup:
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Scripts and data for concatenating and cleaning up the annotations made by snpEff and snpSift.
3_pseudo_id_and_mut_count_for_sim:
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Script and data for variant aggregation and identifying variants that generated.pseudogenes
4_simulation:
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Script and data for simulation to identify genes enriched for mutations.
5_mutational spectra:
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Script and data to extract mutational spectra from vcf files.
6_dNdS:
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Contains script and data to make the dNdS calculations.
7_figures:
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Script and data to generate figures from the paper.
Files
Launay_et_al_Bhinzii.zip
Files
(74.6 MB)
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