(clinker_env) [t6s010062@ln1%bscc-t6 submission_code_work]$ cat > release_minimal/analysis/05_st rain_MAG_WGS/README.md <<'EOF' > # Strain-level and MAG-WGS analyses > > This directory contains the custom scripts used for candidate-species > screening, pairwise normalized genetic-distance calculation, MAG quality > filtering, FastANI analysis, alignment-fraction calculation, and downstream > MAG-WGS clustering. > > Scripts 01-02 summarize the StrainPhlAn results. The standard MetaPhlAn, > sample2markers, extract_markers, and StrainPhlAn commands are described in > the main repository workflow documentation. > > Scripts 03-10 analyze MAG-WGS genomic similarity. Some downstream scripts > use curated metadata-enriched tables generated during project-specific > sample-ID harmonization. These processed tables are treated as analysis > inputs; the historical metadata-curation steps are not included. > > Key thresholds: > MAG quality: completeness >= 70% and contamination <= 10% > Candidate MAG-WGS link: ANI >= 99% and AF >= 0.50 > High-confidence link: ANI >= 99.5% and AF >= 0.70 > StrainPhlAn sharing threshold: nGD < 0.1 > EOF (clinker_env) [t6s010062@ln1%bscc-t6 submission_code_work]$ wc -l release_minimal/figures/Fig6_W GS_clone_plasmid.draft.R 719 release_minimal/figures/Fig6_WGS_clone_plasmid.draft.R (clinker_env) [t6s010062@ln1%bscc-t6 submission_code_work]$ grep -n '^# SOURCE:' \ > release_minimal/figures/Fig6_WGS_clone_plasmid.draft.R 7:# SOURCE: MAKE_Fig6D_plusSlaughter_ARG10_cluster10_circos_MAC.R 280:# SOURCE: MAKE_Fig6E_plusSlaughter_Ecoli_SNP10_ARGassociated_network_clean_MAC_v8_workerW_legendLabel.R (clinker_env) [t6s010062@ln1%bscc-t6 submission_code_work]$ grep -nEi \ > 'Mechanically consolidated|SOURCE:|install\.packages|/public5/home|/Users/|PATH/TO|t6s010062|s etwd\(' \ > release_minimal/figures/Fig6_WGS_clone_plasmid.draft.R \ > | head -n 100 1:# Mechanically consolidated from the final panel scripts listed below. 7:# SOURCE: MAKE_Fig6D_plusSlaughter_ARG10_cluster10_circos_MAC.R 15:FIG6 <"/PATH/TO/mBio_donkey_AMR_figures/Fig6" 280:# SOURCE: MAKE_Fig6E_plusSlaughter_Ecoli_SNP10_ARGassociated_network_clean_MAC_v8_workerW_legendLabel.R 288: install.packages(p, repos = "https://cloud.r-project.org") 300:FIG6 <"/PATH/TO/mBio_donkey_AMR_figures/Fig6" (clinker_env) [t6s010062@ln1%bscc-t6 submission_code_work]$ find staging_v2_1/analysis/05_WGS \ > -maxdepth 1 -type f -printf '%f\n' | sort 01_merge_MOB_PlasmidFinder.py 02_integrate_WGS_annotations.py 03_Ecoli_pairwise_core_SNP.py 04_Kp_pairwise_core_SNP.py 05_Ecoli_clone_events.py 06_Kp_clone_events.py 07_plasmid_cluster_source_summary.py 08_build_key_ARG_matrix.py 09_extract_CTXM_final8_regions.py 10_fix_CTXM_GBK_locus.py 11_patch_CTXM_gene_labels.py 12_format_clinker_gene_labels.py 13_format_clinker_HTML.py 14_build_overview_tree_annotations.R 15_build_coreSNP_tree_annotations.R (clinker_env) [t6s010062@ln1%bscc-t6 submission_code_work]$

(clinker_env) [t6s010062@ln1%bscc-t6 submission_code_work]$ cat > release_minimal/analysis/05_st rain_MAG_WGS/README.md <<'EOF' > # Strain-level and MAG-WGS analyses > > This directory contains the custom scripts used for candidate-species > screening, pairwise normalized genetic-distance calculation, MAG quality > filtering, FastANI analysis, alignment-fraction calculation, and downstream > MAG-WGS clustering. > > Scripts 01-02 summarize the StrainPhlAn results. The standard MetaPhlAn, > sample2markers, extract_markers, and StrainPhlAn commands are described in > the main repository workflow documentation. > > Scripts 03-10 analyze MAG-WGS genomic similarity. Some downstream scripts > use curated metadata-enriched tables generated during project-specific > sample-ID harmonization. These processed tables are treated as analysis > inputs; the historical metadata-curation steps are not included. > > Key thresholds: > MAG quality: completeness >= 70% and contamination <= 10% > Candidate MAG-WGS link: ANI >= 99% and AF >= 0.50 > High-confidence link: ANI >= 99.5% and AF >= 0.70 > StrainPhlAn sharing threshold: nGD < 0.1 > EOF (clinker_env) [t6s010062@ln1%bscc-t6 submission_code_work]$ wc -l release_minimal/figures/Fig6_W GS_clone_plasmid.draft.R 719 release_minimal/figures/Fig6_WGS_clone_plasmid.draft.R (clinker_env) [t6s010062@ln1%bscc-t6 submission_code_work]$ grep -n '^# SOURCE:' \ > release_minimal/figures/Fig6_WGS_clone_plasmid.draft.R 7:# SOURCE: MAKE_Fig6D_plusSlaughter_ARG10_cluster10_circos_MAC.R 280:# SOURCE: MAKE_Fig6E_plusSlaughter_Ecoli_SNP10_ARGassociated_network_clean_MAC_v8_workerW_legendLabel.R (clinker_env) [t6s010062@ln1%bscc-t6 submission_code_work]$ grep -nEi \ > 'Mechanically consolidated|SOURCE:|install\.packages|/public5/home|/Users/|PATH/TO|t6s010062|s etwd\(' \ > release_minimal/figures/Fig6_WGS_clone_plasmid.draft.R \ > | head -n 100 1:# Mechanically consolidated from the final panel scripts listed below. 7:# SOURCE: MAKE_Fig6D_plusSlaughter_ARG10_cluster10_circos_MAC.R 15:FIG6 <"/PATH/TO/mBio_donkey_AMR_figures/Fig6" 280:# SOURCE: MAKE_Fig6E_plusSlaughter_Ecoli_SNP10_ARGassociated_network_clean_MAC_v8_workerW_legendLabel.R 288: install.packages(p, repos = "https://cloud.r-project.org") 300:FIG6 <"/PATH/TO/mBio_donkey_AMR_figures/Fig6" (clinker_env) [t6s010062@ln1%bscc-t6 submission_code_work]$ find staging_v2_1/analysis/05_WGS \ > -maxdepth 1 -type f -printf '%f\n' | sort 01_merge_MOB_PlasmidFinder.py 02_integrate_WGS_annotations.py 03_Ecoli_pairwise_core_SNP.py 04_Kp_pairwise_core_SNP.py 05_Ecoli_clone_events.py 06_Kp_clone_events.py 07_plasmid_cluster_source_summary.py 08_build_key_ARG_matrix.py 09_extract_CTXM_final8_regions.py 10_fix_CTXM_GBK_locus.py 11_patch_CTXM_gene_labels.py 12_format_clinker_gene_labels.py 13_format_clinker_HTML.py 14_build_overview_tree_annotations.R 15_build_coreSNP_tree_annotations.R (clinker_env) [t6s010062@ln1%bscc-t6 submission_code_work]$