Merge pull request #9 from raphenya/main

adds scrips and outputs for utility of the dataset
AMR-Hackathon-2021 · May 12, 2022 · 55da99b · 55da99b
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diff --git a/utility_of_the_dataset/README.md b/utility_of_the_dataset/README.md
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+#### Comparing AMR tools
+
+We compared AMR tools before choosing one to produce the benchmarking datasets.
+We used the hAMRonization workflow (https://github.com/pha4ge/hAMRonization) for this task. The hAMRonization workflow uses 12 different AMR tools to predict AMR genes in genomic data and produces a standard report to compare results across the tools.
+
+#### Data
+
+We analysed 94 assembled genomes downloaded from NCBI.
+
+#### Analysis
+
+1. Generate data for radar plot using the following:
+
+```
+python3 scripts/radar_plot_data.py > analysis/radar_data_94_samples.tsv
+```
+
+2. Generate data for sankey plot using the following:
+
+```
+python3 scripts/merge_hamronized_reports.py
+```
+
+
+#### Results (in analysis directory)
+
+- radar_data_94_samples.tsv
+- sankey_data_94_samples.tsv
+
diff --git a/utility_of_the_dataset/analysis/5_amr_tools_94_samples.png b/utility_of_the_dataset/analysis/5_amr_tools_94_samples.png
diff --git a/utility_of_the_dataset/analysis/5_amr_tools_94_samples.svg b/utility_of_the_dataset/analysis/5_amr_tools_94_samples.svg
diff --git a/utility_of_the_dataset/analysis/5_amr_tools_94_samples_sankey.png b/utility_of_the_dataset/analysis/5_amr_tools_94_samples_sankey.png
diff --git a/utility_of_the_dataset/analysis/5_amr_tools_94_samples_sankey.svg b/utility_of_the_dataset/analysis/5_amr_tools_94_samples_sankey.svg