Proximeta Results Manifest

The following manifest lists all files found in the ProxiMeta tarball:

sample-name_all_files.tar.gz

Main directory

The file contains 6 tarballs.

folder name	source tarball
inputs	sample-name_amr_files.tar.gz
microbial_genomes	sample-name_input_files.tar.gz
sample-name_AMR_Files	sample-name_metabolism_files.tar.gz
sample-name_Metabolism_Files	sample-name_microbial_genome_files.tar.gz
sample-name_Plasmid_Files	sample-name_plasmid_files.tar.gz
sample-name_Viral_Files	sample-name_viral_files.tar.gz

Inputs

all//inputs:

• sample-name_contigs.fasta
• sample-name_s3_m1.bam

Microbial Genomes

all//microbial_genomes:

• sample-name_clusters
  • bin_x.fasta
  • …
• sample-name_proximeta_report.tsv

AMR Files

all//sample-name_AMR_Files:

• amr_annotations/
  • AMR_annotations_summary.tsv
• amr_host_connections/
  • amr_gene_to_host_summary.tsv
  • amr_host_content.tsv
  • heatmaps/
    • amr_contig_to_host_heatmap.png
    • amr_contig_to_host_matrix.tsv
    • amr_gene_to_host_heatmap.png
    • amr_gene_to_host_matrix.tsv

Metabolism Files

all//sample-name_Metabolism_Files:

• metabolism_results/
  • cluster_annotation_gff/
    • bin_x.gff
    • …
  • cluster_modules_matrix_complete.tsv
  • cluster_protein_sequences/
    • bin_x.faa
    • …
  • cluster_module_completion/
    • bin_x.tsv
    • …
  • cluster_pathways_info
    • bin_x.tsv
    • …
  • cluster_search_results
    • bin_x.blast.tsv
    • …
  • cluster_modules_matrix_complete.png
  • cluster_pathways_plots
    • bin_x
      • map000n.pathview.png

Plasmid Files

all//sample-name_Plasmid_Files:

• ProxiphageDocumentationPlasmid.html
• plasmid_MAGs/
  • binned_plasmid_contigs_summary.tsv
  • figures/
    • plasmid_quality_barplot.png
    • plasmid_quality_plot.png
  • pMAG_sequences/
    • pMAG_x.fasta
    • …
  • plasmid_mags_summary.tsv
• plasmid_hosts/
  • figures/
    • plasmid_heatmap_mobile_element_copies_per_cell.png
    • plasmid_host_count_histogram.png
    • plasmid_histogram_mobile_element_copies_per_cell.png
  • plasmid_host_associations_filtered.tsv
  • plasmid_host_associations_unfiltered.tsv
• pMAG_hosts/
  • pMAG_host_associations_filtered.tsv
  • pMAG_host_associations_unfiltered.tsv
  • figures/
    • pMAG_heatmap_mobile_element_copies_per_cell.png
    • pMAG_host_count_histogram.png
    • pMAG_histogram_mobile_element_copies_per_cell.png
• plasmid_annotations/
  • integrated_plasmid_annotation_summary.tsv
  • plasmid_annotation_summary.tsv
  • integrated_plasmid_contigs.fasta
  • plasmid_contigs.fasta

Viral Files

all//sample-name_Viral_Files:

• ProxiphageDocumentationVirus.html
• viral_MAGs
  • binned_viral_contigs_summary.tsv
  • figures/
    • viral_quality_barplot.png
    • viral_quality_plot.png
  • vMAG_sequences
    • vMAG_x.fasta
  • viral_mags_summary.tsv
• viral_hosts
  • figures/
    • viral_heatmap_mobile_element_copies_per_cell.png
    • viral_host_count_histogram.png
    • viral_histogram_mobile_element_copies_per_cell.png
  • viral_host_associations_filtered.tsv
  • viral_host_associations_unfiltered.tsv
• vMAG_hosts
  • figures/
    • vMAG_heatmap_mobile_element_copies_per_cell.png
    • vMAG_host_count_histogram.png
    • vMAG_histogram_mobile_element_copies_per_cell.png
  • vMAG_host_associations_filtered.tsv
  • vMAG_host_associations_unfiltered.tsv
• viral_annotations
  • all_viral_contigs.fasta
  • prophage_sequences.fasta
  • viral_annotations_summary.tsv
  • viral_protein_annotations.tsv