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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.

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Name		Name	Last commit message	Last commit date
Latest commit History 8 Commits
01_fastqc_to_AMR_genes.bash		01_fastqc_to_AMR_genes.bash
AMRgenes_heatmap2.R		AMRgenes_heatmap2.R
README.md		README.md
correlation_plots_more_beta_lactams_new_data.R		correlation_plots_more_beta_lactams_new_data.R

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AMR_correlation

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.

Packages used:

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

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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.

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