Code for analyzing Bartonella bacteria genomes for simple-sequence repeats that may function as contingency loci.
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.
Illumina sequencing reads used as input to create the assemblies of the 38 Bartonella isolates from the Negev Desert sand dunes are available for download from the NCBI SRA (PRJNA1061316).