This is the code used to process fastq files of 147 bovine Escherichia coli isolates to de-novo assembled genomes, followed by screening for antimicrobial resistance genes and data analysis to correlate with phenotypic AMR data.
- FastQc v0.11.8
- fastp v0.20.0
- SPAdes v3.13.1
- Quast v5.0.2
- abricate v1.0.0 https://github.com/tseemann/abricate
- mlst v2.18.1 https://github.com/tseemann/mlst
- AMRFinder Plus v3.8.4