Code for analyzing next-generation DNA sequencing data to predict mutations that evolved during passaging of Bartonella krasnovii bacteria through rodents in the laboratory.
Parasite contingency loci and the evolution of host specificity: Bartonella krasnovii adaptation to a rodent host is dominated by mutations in simple-sequence repeats in an adhesin gene
Ruth Rodríguez‑Pastor, Nadav Knossow, Naama Shahar, Adam Z. Hasik, Daniel E. Deatherage, Ricardo Gutiérrez, Shimon Harrus, Luis Zaman, Richard E. Lenski, Jeffrey E. Barrick, Hadas Hawlena
Each folder is a step in the analysis.
It may contain a Conda environment, bash command file, and input/output data files needed to carry out that step of the analysis. Usually, you will need to copy/move the output from one folder to the next.
The Illumina sequencing reads used as input in the first step are available for download from the NCBI SRA (PRJNA914220).