Files in joelewis101/blantyreESBL
Data and Code Repository For a Study Describing Antimicrobial Resistance in Blantyre, Malawi

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CHANGELOG.md

DESCRIPTION

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LICENSE.md

NAMESPACE

R/data.R README.Rmd README.md

_pkgdown.yml

blantyreESBL.Rproj

data-raw/.gitignore

data-raw/all_dassim_kleb_and_esco_accession.csv

data-raw/amr_genes/esco-amr-ariba-report-part1.csv

data-raw/amr_genes/esco-amr-ariba-report-part2.csv

data-raw/amr_genes/kleb-amr-ariba-report.csv

data-raw/btESBL_model2simulations.rda

data-raw/contig_clusters/contigs-CMY_42.clust.clstr.tsv

data-raw/contig_clusters/contigs-CTX_M_1.clust.clstr.tsv

data-raw/contig_clusters/contigs-CTX_M_14.clust.clstr.tsv

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data-raw/contig_clusters/contigs-CTX_M_27.clust.clstr.tsv

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data-raw/core_gene_trees/esco_core_gene_tree.treefile

data-raw/core_gene_trees/esco_core_gene_tree_nonASC.treefile

data-raw/core_gene_trees/kleb_core_gene_tree.treefile

data-raw/core_gene_trees/kleb_core_gene_tree_nonASC.treefile

data-raw/ecoli-genomics-paper/2021-09-06_CARD-QRDR-mutations.csv

data-raw/ecoli-genomics-paper/F1_genome_metadata.csv

data-raw/ecoli-genomics-paper/IQTREE_globaltree.treefile

data-raw/ecoli-genomics-paper/QRDR_ariba_output.tsv

data-raw/ecoli-genomics-paper/QUAST_report1.tsv

data-raw/ecoli-genomics-paper/QUAST_report2.tsv

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data-raw/ecoli-genomics-paper/all_dassim_esco_vf_ariba.csv

data-raw/ecoli-genomics-paper/horesh_full_diversity/.gitignore

data-raw/ecoli-genomics-paper/horesh_full_diversity/2021-10-13horesh_genomes_sampled.txt

data-raw/ecoli-genomics-paper/horesh_full_diversity/2021-10-13horesh_genomes_sampled_filestem.txt

data-raw/ecoli-genomics-paper/horesh_full_diversity/FINAL_METADATA_CLEANED.tsv

data-raw/ecoli-genomics-paper/horesh_full_diversity/analysis_2021-11-03_110200_phylogroups.txt

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data-raw/ecoli-genomics-paper/horesh_full_diversity/horesh_read_filepaths.txt

data-raw/ecoli-genomics-paper/horesh_full_diversity/mung_horesh_metadata.R

data-raw/ecoli-genomics-paper/horesh_full_diversity/read_filepaths_for_ariba.txt

data-raw/ecoli-genomics-paper/horesh_full_diversity/read_filepaths_for_shreddding.txt

data-raw/ecoli-genomics-paper/mlst.csv

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data-raw/ecoli-genomics-paper/musicha_mlst.csv

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data-raw/included_lanes/kleb_lanes_retained_following_qc.txt

data-raw/kleb-genomics-paper/.gitignore

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data-raw/kleb-genomics-paper/vfdb_vfid_downloads.csv

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data-raw/plasmids/D1ariba_plasmidfinder_clustsmall.csv

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data-raw/review_comment_work/contig_msa/CTX_M_15.10.samlog

data-raw/review_comment_work/contig_msa/CTX_M_15.10.txt

data-raw/review_comment_work/contig_msa/CTX_M_15.10_rep.fa

data-raw/review_comment_work/contig_msa/CTX_M_15.10_rep.txt

data-raw/review_comment_work/contig_msa/CTX_M_15.113.fa

data-raw/review_comment_work/contig_msa/CTX_M_15.113.filtered.sam

data-raw/review_comment_work/contig_msa/CTX_M_15.113.paf

data-raw/review_comment_work/contig_msa/CTX_M_15.113.paflog

data-raw/review_comment_work/contig_msa/CTX_M_15.113.sam

data-raw/review_comment_work/contig_msa/CTX_M_15.113.samlog

data-raw/review_comment_work/contig_msa/CTX_M_15.113.txt

data-raw/review_comment_work/contig_msa/CTX_M_15.113_rep.fa

data-raw/review_comment_work/contig_msa/CTX_M_15.113_rep.txt

data-raw/review_comment_work/contig_msa/CTX_M_15.123.fa

data-raw/review_comment_work/contig_msa/CTX_M_15.123.filtered.sam

data-raw/review_comment_work/contig_msa/CTX_M_15.123.paf

data-raw/review_comment_work/contig_msa/CTX_M_15.123.paflog

data-raw/review_comment_work/contig_msa/CTX_M_15.123.sam

data-raw/review_comment_work/contig_msa/CTX_M_15.123.samlog

data-raw/review_comment_work/contig_msa/CTX_M_15.123.txt

data-raw/review_comment_work/contig_msa/CTX_M_15.123_rep.fa

data-raw/review_comment_work/contig_msa/CTX_M_15.123_rep.txt

data-raw/review_comment_work/contig_msa/CTX_M_15.29.fa

data-raw/review_comment_work/contig_msa/CTX_M_15.29.filtered.sam

data-raw/review_comment_work/contig_msa/CTX_M_15.29.paf

data-raw/review_comment_work/contig_msa/CTX_M_15.29.paflog

data-raw/review_comment_work/contig_msa/CTX_M_15.29.sam

data-raw/review_comment_work/contig_msa/CTX_M_15.29.samlog

data-raw/review_comment_work/contig_msa/CTX_M_15.29.txt

data-raw/review_comment_work/contig_msa/CTX_M_15.29_rep.fa

data-raw/review_comment_work/contig_msa/CTX_M_15.29_rep.txt

data-raw/review_comment_work/contig_msa/CTX_M_15.41.fa

data-raw/review_comment_work/contig_msa/CTX_M_15.41.filtered.sam

data-raw/review_comment_work/contig_msa/CTX_M_15.41.paf

data-raw/review_comment_work/contig_msa/CTX_M_15.41.paflog

data-raw/review_comment_work/contig_msa/CTX_M_15.41.sam

data-raw/review_comment_work/contig_msa/CTX_M_15.41.samlog

data-raw/review_comment_work/contig_msa/CTX_M_15.41.txt

data-raw/review_comment_work/contig_msa/CTX_M_15.41_rep.fa

data-raw/review_comment_work/contig_msa/CTX_M_15.41_rep.txt

data-raw/review_comment_work/contig_msa/CTX_M_15.61.fa

data-raw/review_comment_work/contig_msa/CTX_M_15.61.filtered.sam

data-raw/review_comment_work/contig_msa/CTX_M_15.61.paf

data-raw/review_comment_work/contig_msa/CTX_M_15.61.paflog

data-raw/review_comment_work/contig_msa/CTX_M_15.61.sam

data-raw/review_comment_work/contig_msa/CTX_M_15.61.samlog

data-raw/review_comment_work/contig_msa/CTX_M_15.61.txt

data-raw/review_comment_work/contig_msa/CTX_M_15.61_rep.fa

data-raw/review_comment_work/contig_msa/CTX_M_15.61_rep.txt

data-raw/review_comment_work/contig_msa/CTX_M_15.66.fa

data-raw/review_comment_work/contig_msa/CTX_M_15.66.filtered.sam

data-raw/review_comment_work/contig_msa/CTX_M_15.66.paf

data-raw/review_comment_work/contig_msa/CTX_M_15.66.paflog

data-raw/review_comment_work/contig_msa/CTX_M_15.66.sam

data-raw/review_comment_work/contig_msa/CTX_M_15.66.samlog

data-raw/review_comment_work/contig_msa/CTX_M_15.66.txt

data-raw/review_comment_work/contig_msa/CTX_M_15.66_rep.fa

data-raw/review_comment_work/contig_msa/CTX_M_15.66_rep.txt

data-raw/review_comment_work/contig_msa/CTX_M_15.69.fa

data-raw/review_comment_work/contig_msa/CTX_M_15.69.filtered.sam

data-raw/review_comment_work/contig_msa/CTX_M_15.69.paf

data-raw/review_comment_work/contig_msa/CTX_M_15.69.paflog

data-raw/review_comment_work/contig_msa/CTX_M_15.69.sam

data-raw/review_comment_work/contig_msa/CTX_M_15.69.samlog

data-raw/review_comment_work/contig_msa/CTX_M_15.69.txt

data-raw/review_comment_work/contig_msa/CTX_M_15.69_rep.fa

data-raw/review_comment_work/contig_msa/CTX_M_15.69_rep.txt

data-raw/review_comment_work/contig_msa/CTX_M_27.1.fa

data-raw/review_comment_work/contig_msa/CTX_M_27.1.filtered.sam

data-raw/review_comment_work/contig_msa/CTX_M_27.1.paf

data-raw/review_comment_work/contig_msa/CTX_M_27.1.paflog

data-raw/review_comment_work/contig_msa/CTX_M_27.1.sam

data-raw/review_comment_work/contig_msa/CTX_M_27.1.samlog

data-raw/review_comment_work/contig_msa/CTX_M_27.1.txt

data-raw/review_comment_work/contig_msa/CTX_M_27.1_rep.fa

data-raw/review_comment_work/contig_msa/CTX_M_27.1_rep.txt

data-raw/review_comment_work/contig_msa/SHV_12.1.fa

data-raw/review_comment_work/contig_msa/SHV_12.1.filtered.sam

data-raw/review_comment_work/contig_msa/SHV_12.1.paf

data-raw/review_comment_work/contig_msa/SHV_12.1.paflog

data-raw/review_comment_work/contig_msa/SHV_12.1.sam

data-raw/review_comment_work/contig_msa/SHV_12.1.samlog

data-raw/review_comment_work/contig_msa/SHV_12.1.txt

data-raw/review_comment_work/contig_msa/SHV_12.1_rep.fa

data-raw/review_comment_work/contig_msa/SHV_12.1_rep.txt

data-raw/review_comment_work/contig_msa/alignments/CTX_M_15.10.aln

data-raw/review_comment_work/contig_msa/alignments/CTX_M_15.10/CTX_M_15.10.mod.aln

data-raw/review_comment_work/contig_msa/alignments/CTX_M_15.113.aln

data-raw/review_comment_work/contig_msa/alignments/CTX_M_15.113/CTX_M_15.113.mod.aln

data-raw/review_comment_work/contig_msa/alignments/CTX_M_15.123.aln

data-raw/review_comment_work/contig_msa/alignments/CTX_M_15.123/CTX_M_15.123.mod.aln

data-raw/review_comment_work/contig_msa/alignments/CTX_M_15.29.aln

data-raw/review_comment_work/contig_msa/alignments/CTX_M_15.29/CTX_M_15.29.mod.aln

data-raw/review_comment_work/contig_msa/alignments/CTX_M_15.41.aln

data-raw/review_comment_work/contig_msa/alignments/CTX_M_15.41/CTX_M_15.41.mod.aln

data-raw/review_comment_work/contig_msa/alignments/CTX_M_15.61.aln

data-raw/review_comment_work/contig_msa/alignments/CTX_M_15.61/CTX_M_15.61.mod.aln

data-raw/review_comment_work/contig_msa/alignments/CTX_M_15.66.aln

data-raw/review_comment_work/contig_msa/alignments/CTX_M_15.66/CTX_M_15.66.mod.aln

data-raw/review_comment_work/contig_msa/alignments/CTX_M_15.69.aln

data-raw/review_comment_work/contig_msa/alignments/CTX_M_15.69/CTX_M_15.69.mod.aln

data-raw/review_comment_work/contig_msa/alignments/CTX_M_27.1.aln

data-raw/review_comment_work/contig_msa/alignments/CTX_M_27.1/CTX_M_27.1.mod.aln

data-raw/review_comment_work/contig_msa/alignments/SHV_12.1.aln

data-raw/review_comment_work/contig_msa/alignments/SHV_12.1/SHV_12.1.mod.aln

data-raw/review_comment_work/contig_msa/alignments/prep_alignments_for_plotting.sh

data-raw/review_comment_work/contig_msa/alignments/readme.txt

data-raw/review_comment_work/contig_sens_ax/len_diff_0.2_contigs-CMY_42.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.2_contigs-CTX_M_1.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.2_contigs-CTX_M_14.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.2_contigs-CTX_M_15.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.2_contigs-CTX_M_16.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.2_contigs-CTX_M_27.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.2_contigs-CTX_M_3.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.2_contigs-CTX_M_55.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.2_contigs-CTX_M_65.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.2_contigs-CTX_M_9.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.2_contigs-SHV_12.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.2_contigs-SHV_27.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.2_contigs-SHV_38.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.2_contigs-SHV_40.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.2_contigs-SHV_41.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.2_contigs-SHV_70.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.2_contigs-SHV_98.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.2_contigs-SHV_99.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.4_contigs-CMY_42.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.4_contigs-CTX_M_1.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.4_contigs-CTX_M_14.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.4_contigs-CTX_M_15.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.4_contigs-CTX_M_16.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.4_contigs-CTX_M_27.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.4_contigs-CTX_M_3.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.4_contigs-CTX_M_55.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.4_contigs-CTX_M_65.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.4_contigs-CTX_M_9.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.4_contigs-SHV_12.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.4_contigs-SHV_27.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.4_contigs-SHV_38.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.4_contigs-SHV_40.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.4_contigs-SHV_41.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.4_contigs-SHV_70.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.4_contigs-SHV_98.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.4_contigs-SHV_99.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.6_contigs-CMY_42.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.6_contigs-CTX_M_1.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.6_contigs-CTX_M_14.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.6_contigs-CTX_M_15.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.6_contigs-CTX_M_16.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.6_contigs-CTX_M_27.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.6_contigs-CTX_M_3.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.6_contigs-CTX_M_55.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.6_contigs-CTX_M_65.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.6_contigs-CTX_M_9.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.6_contigs-SHV_12.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.6_contigs-SHV_27.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.6_contigs-SHV_38.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.6_contigs-SHV_40.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.6_contigs-SHV_41.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.6_contigs-SHV_70.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.6_contigs-SHV_98.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.6_contigs-SHV_99.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.8_contigs-CMY_42.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.8_contigs-CTX_M_1.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.8_contigs-CTX_M_14.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.8_contigs-CTX_M_15.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.8_contigs-CTX_M_16.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.8_contigs-CTX_M_27.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.8_contigs-CTX_M_3.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.8_contigs-CTX_M_55.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.8_contigs-CTX_M_65.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.8_contigs-CTX_M_9.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.8_contigs-SHV_12.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.8_contigs-SHV_27.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.8_contigs-SHV_38.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.8_contigs-SHV_40.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.8_contigs-SHV_41.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.8_contigs-SHV_70.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.8_contigs-SHV_98.tsv

data-raw/review_comment_work/contig_sens_ax/len_diff_0.8_contigs-SHV_99.tsv

data-raw/review_comment_work/contig_sens_ax/load_contig_sens_ax_data_fn.R

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.96_contigs-CMY_42.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.96_contigs-CTX_M_1.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.96_contigs-CTX_M_14.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.96_contigs-CTX_M_15.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.96_contigs-CTX_M_16.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.96_contigs-CTX_M_27.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.96_contigs-CTX_M_3.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.96_contigs-CTX_M_55.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.96_contigs-CTX_M_65.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.96_contigs-CTX_M_9.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.96_contigs-SHV_12.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.96_contigs-SHV_27.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.96_contigs-SHV_38.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.96_contigs-SHV_40.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.96_contigs-SHV_41.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.96_contigs-SHV_70.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.96_contigs-SHV_98.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.96_contigs-SHV_99.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.97_contigs-CMY_42.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.97_contigs-CTX_M_1.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.97_contigs-CTX_M_14.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.97_contigs-CTX_M_15.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.97_contigs-CTX_M_16.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.97_contigs-CTX_M_27.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.97_contigs-CTX_M_3.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.97_contigs-CTX_M_55.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.97_contigs-CTX_M_65.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.97_contigs-CTX_M_9.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.97_contigs-SHV_12.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.97_contigs-SHV_27.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.97_contigs-SHV_38.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.97_contigs-SHV_40.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.97_contigs-SHV_41.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.97_contigs-SHV_70.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.97_contigs-SHV_98.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.97_contigs-SHV_99.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.98_contigs-CMY_42.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.98_contigs-CTX_M_1.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.98_contigs-CTX_M_14.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.98_contigs-CTX_M_15.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.98_contigs-CTX_M_16.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.98_contigs-CTX_M_27.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.98_contigs-CTX_M_3.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.98_contigs-CTX_M_55.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.98_contigs-CTX_M_65.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.98_contigs-CTX_M_9.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.98_contigs-SHV_12.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.98_contigs-SHV_27.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.98_contigs-SHV_38.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.98_contigs-SHV_40.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.98_contigs-SHV_41.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.98_contigs-SHV_70.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.98_contigs-SHV_98.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.98_contigs-SHV_99.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.99_contigs-CMY_42.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.99_contigs-CTX_M_1.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.99_contigs-CTX_M_14.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.99_contigs-CTX_M_15.tsv

data-raw/review_comment_work/contig_sens_ax/seq_ident_0.99_contigs-CTX_M_16.tsv

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Data and Code Repository For a Study Describing Antimicrobial Resistance in Blantyre, Malawi

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