This repository to complimemt the publication "Exploring the Antibiotic Resistance Burden in Livestock, Livestock Handlers and Their Non-Livestock Handling Contacts: A One Health Perspective" by Hickman et. al 2021 (https://www.frontiersin.org/articles/10.3389/fmicb.2021.651461/full)
All raw sequence data can be obtained from the European Nucleotide Archive (ENA) under the project accession number PRJEB38313.
All Genomic data processing was performed on the high computing capacity provided by SNIC through Uppsala Multidisciplinary Centre for Advance Computational Science (UPPMAX). Under the computational project SNIC2019-8-275 and small storage - Uppstore2019121
All processing of the whole genome sequences was done with open software with an in-house bioinformatics pipeline. Our pipeline consists of four main modules: Dependencies listed below.
- For quality control (QC) assessment of the raw sequence files and trimming the sequence reads
- FastQC (Wingett and Andrews, 2018)
- MultiQC (Ewels et al., 2016)
- Trim Galore (Babraham Bioinformatics, 2020)
- De novo assembly with assembly QC
- Unicycler (Wick et al., 2017)
- QUAST (Gurevich et al., 2013)
- MultiQC (Ewels et al., 2016)
- Molecular output excel report of genomic data
- KmerFinder (Larsen et al., 2014)
- ARIBA (Hunt et al., 2017)
- ResFinder (Zankari et al., 2012)
- PointFinder (Zankari et al., 2017)
- A core genome maximum likelihood phylogenetic tree
- Prokka (Seemann, 2014)
- Roary (Page et al., 2015)
- IQ-Tree2 (Quang et al., 2020)
Downstream figure production and visualization was done locally via python scripts with the exception of the phylogenetic tree which was produced in iTOL web platform (Letunic and Bork, 2019).