GitHub Repository for: Comparative genomics reveals phylogenetic intermixing of Stomoxys fly, manure, and bovine mastitis-associated bacteria in dairy settings

<h3>Overview</h3><p dir="ltr">Comparative genomic analysis of bacterial strains isolated from <i>Stomoxys</i> (stable) flies and manure samples collected on a Wisconsin dairy farm. The repository contains code used for analysis of genomic read data and generation of associated figures.</p><h3>Availability of Sequence Data</h3><p dir="ltr">Raw Illumina reads and assemblies are available in the NCBI Sequence Read Archive (<a href="https://www.ncbi.nlm.nih.gov/sra" rel="nofollow" target="_blank">https://www.ncbi.nlm.nih.gov/sra</a>) under BioProject ID PRJNA1216036.</p><h3>Folder Structure</h3><p dir="ltr"><b>01</b> - FASTQ file trimming and quality control (FastQC)<br><b>02</b> - Assembly (Shovill/SPAdes) and annotation (Prokka) along with associated quality control checks (Quast, BUSCO)<br><b>03</b> - Typing (Kleborate, ClermonTyping, MLST) and screening of contigs for VFs (vfdb/VirulenceFinder) and ARGs (Abricate)<br><b>04</b> - Core genome alignment and FastTree of sequenced <i>Escherichia</i> <i>coli</i> and <i>Klebsiella </i><i>pneumoniae</i><br><b>05</b> - Selection of NCBI genome sets and associated phylogenetic tree construction<br><b>06</b> - Functional annotation (eggNOG-mapper) of <i>Mammaliicoccus</i><i> sciuri</i><br><b>07</b> - Strain and ARG-encoding plasmid comparisons (Mummer4)<br><b>Figures</b> - Contain R Scripts, TreeViewer, and needed import files to recreate figures in the manuscript</p>