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4). Output

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Duncan Berger edited this page Sep 8, 2024 · 4 revisions

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Output folder structure

LOMA will output files per-metric/tool as well as a series of summary reports. Outputs can be found in the directory specified by the '--outdir' parameter (default: 'results'). Results are separated by RUN_ID, then SAMPLE_ID and finally by approach and metric. A summary of the folder structure can be found below.

Output folder structure overview

docs_images_loma_file_structure

Summary HTML reports

A series of HTML summary reports can be found in the 'summary' directory, these cover the major areas of interest when sequencing metagenomic samples and should assist in assessing sequencing data quality, sample composition and perform various types of in silico phenotyping.

<SAMPLE_ID>.<RUN_ID>.summary_report.html

  • Simiplified summary detailing all major metrics/results of interest, for an overall sample summary. These results include:
    • Quality Control
      • Read quality information (pre- and post-quality control)
    • Taxonomic Summary - Targets only ()
      • Read-based taxonomic summary - Subset to target species' only
    • Taxonomic Summary - All results ()
      • Read-based taxonomic summary - All results
    • Assembly Summary
      • Assembly statistics for the entire metagenome assembly
    • Binning Summary
      • Summary of proportion of the entire metagenome assembly assigned to a metagenome assembled genome (MAG) (i.e binned)
    • Bin Quality Control
      • Quality statistics and taxonomic assignments for each MAG
    • Sequence Typing (bins)
      • Results of multi-Locus sequence typing
    • Antimicrobial Resistance (bins)
      • Screens for antimicrobial resistance genes/mutations.
    • Target Genes (bins)
      • Screens for genes of interest using user supplied databases
    • Escherichia coli / Shigella spp. typing (bins)
      • Performs analysis specific to Escherichia coli_ / _Shigella spp.
    • Samonella typing (bins)
      • Performs analysis specific to Salmonella spp.
    • Listeria monocytogenes Typing (bins)
      • Performs analysis specific to Listeria monocytogenes

<SAMPLE_ID>.<RUN_ID>.readqc_report.html

  • Read quality metrics, pre- and post- quality control.

<SAMPLE_ID>.<RUN_ID>.taxonomy_report.html

  • Read-based taxonomic abundance for Kraken2, Centrifuger and/or Sylph (depending on which tools were used), including both:
    • Assignments rates per taxonomic rank
    • Species abundance estimates

<SAMPLE_ID>.<RUN_ID>.amr_report.html

  • Results of AMR typing tools (ABRicate, AMRFinderPlus, ResFinder and RGI)
  • Reported per-tool in two formats:
    • Summary report - All identified AMR genes/drug-classes per-bin.
    • Detailed report - All identified AMR genes, listed per-gene/drug-class/mutation.

<SAMPLE_ID>.<RUN_ID>.summary_binning_report.html

  • Summary of binning results, including:
    • Binning summary - Interactive summary plots of all contigs/bins, including taxonomic assignments, bin and contig quality
    • Binning statistics - Table of quality metrics reported per-bin
    • Bin Quality Control - Plots of bin summary and range of quality metrics across all bins
    • Contig Statistics - Contig quality metrics and taxonomic classifications (per-contig)

Per-metric files

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