Proximeta Results Manifest

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