Welcome to metator’s documentation!

Tutorial

• Tutorial MetaTOR
  • Table of contents
  • Input data
  • A. Quick start
    • 1. Simplest command
    • 2. Main output files
  • B. A multiple modules pipeline
    • 1. Choose your starting point
    • 2. Skip the validation module
    • 3. Launch the modules separately
  • C. Advanced parameters
    • 1. Digestion site
    • 2. Binning parameters
  • D. Analysing the output
  • References

Manual curation of Metator MAGs

• Manual curation of the contaminated MetaTOR MAGs with anvio
  • Table of contents
  • Requirements
  • Input data
  • A. Build anvio database
    • Build the contigs database
    • Runs the hmm profiles and definde the taxonomy with anvio
  • B. Build anvio coverage profile
    • Prepare the alignment files
    • Build the coverage profile
    • Import binning
  • C. Refine the bins
    • Manual refinement of the bins
    • Export the new binning
    • Output analysis
  • References

MAGs visualization and scaffolding

• MAG visualization and scaffolding
  • Table of contents
  • Requirements
  • Input data
  • A. Build the HiC contact map
    • Using pairix index
  • B. Visualization of the contact map
  • C. Scaffolding of the contact map
  • References

Reference API

• metator package
  • Submodules
  • metator.align module
    • align()
    • get_contact_pairs()
    • merge_alignment()
    • process_bamfile()
    • process_bwa_bamfile()
  • metator.commands module
    • AbstractCommand
      • AbstractCommand.check_output_path()
      • AbstractCommand.execute()
    • Contactmap
      • Contactmap.execute()
    • Network
      • Network.execute()
    • Pairs
      • Pairs.execute()
    • Partition
      • Partition.execute()
    • Pipeline
      • Pipeline.execute()
    • Qc
      • Qc.execute()
    • Scaffold
      • Scaffold.execute()
    • Validation
      • Validation.execute()
    • generate_log_footer()
    • generate_log_header()
  • metator.contact_map module
    • MetatorObject
      • MetatorObject.get_contigs_data()
      • MetatorObject.set_contigs()
      • MetatorObject.set_large_contigs()
      • MetatorObject.set_metator_object()
      • MetatorObject.write_fasta()
    • extract_pairs()
    • generate_contact_map()
  • metator.figures module
    • build_matrix_network()
    • figure_camembert_quality()
    • figures_bins_distribution()
    • figures_bins_size_distribution()
    • figures_mags_GC_boxplots()
    • figures_mags_HiC_cov_boxplots()
    • figures_mags_SG_cov_boxplots()
    • generates_frags_network()
    • network_heatmap()
    • plot_figures()
    • reindex_df()
  • metator.io module
    • check_checkm()
    • check_fasta_index()
    • check_is_fasta()
    • check_louvain_cpp()
    • check_pairix()
    • check_pairtools()
    • generate_fasta_index()
    • generate_temp_dir()
    • get_pairs_data()
    • get_restriction_site()
    • getrandbits()
    • micomplete_results_to_dict()
    • read_bin_summary()
    • read_compressed()
    • read_contig_data()
    • read_results_checkm()
    • retrieve_fasta()
    • save_sparse_matrix()
    • sort_pairs()
    • sort_pairs_pairtools()
    • write_bin_summary()
  • metator.log module
    • set_file_handler()
    • setup_text_logging()
  • metator.main module
    • main()
  • metator.network module
    • alignment_to_contacts()
    • compute_network()
    • create_contig_data()
    • normalize_pair()
    • precompute_network()
    • write_contig_data()
    • write_hit_data()
  • metator.partition module
    • algo_partition()
    • build_clustering_matrix()
    • defined_overlapping_bins()
    • detect_core_bins()
    • generate_fasta()
    • get_distances_splitmat()
    • get_hamming_distance()
    • leiden_iterations_java()
    • louvain_iterations_cpp()
    • partition()
    • remove_isolates()
    • spinglass_partition()
    • update_contigs_data()
  • metator.validation module
    • checkm()
    • checkm_compare_bins()
    • correct_final_bin()
    • get_bin_coverage()
    • give_results_info()
    • merge_micomplete()
    • micomplete_compare_bins()
    • micomplete_quality()
    • recursive_clustering()
    • recursive_clustering_worker()
    • recursive_decontamination()
    • update_contigs_data_recursive()
    • write_bins_contigs()
  • metator.version module
  • Module contents

Indices and tables

• Index

• Module Index

• Search Page