Sample results
For each sample, a folder is created with results from various tools, as follows:
- amr - Predictions of antimicrobial resistance genes
- abricate - Results from Abricate
- amrfinderplus - Results from AMFfinderPlus
- annotation - Gene model predictions
- prokka - Prokka annotations
- assembly - The genome assembly and related information
- busco - Busco analysis of gene space coverage
- quast - Quast assembly metrics
- flye/dragonflye/shovill - the assembler output(s)
- mlst - MLST typing results
- Plamids - Identification of plasmids from the assembly
- qc - Basic read QC
- fastqc - Quality metrics of reads
- confindr_results - ConfindR contamination check
- taxonomy - Taxonomic profiling using raw reads
- kraken2 - Results from Kraken2
- sample.json - A coarse summary of various sample-level results
Combined results
Some results are computed for all samples of a run, or for all samples belonging to the same species. These results are as follows:
- cgMLST - core genome MLST calls
- chewbbaca - Results from Chewbbaca across all samples from the same species, including minimal spanning tree and distance matrix
- pymlst - Results from pyMLST across all samples from the same species (distance matrix only)
- AMR
- Aggregated results from supported antimicrobial resistance gene predictors
MultiQC
- run_name_multiqc_report.html - Sample-level summary
- Illumina - QC metrics relating to Illumina data
- Nanopore - QC metrics relating to Nanopore data
- Pacbio - QC metrics relating to Pacbio data
pipeline_info
This folder contains the pipeline run metrics
- pipeline_dag.svg - the workflow graph (only available if GraphViz is installed)
- pipeline_report.html - the (graphical) summary of all completed tasks and their resource usage
- pipeline_report.txt - a short summary of this analysis run in text format
- pipeline_timeline.html - chronological report of compute tasks and their duration
- pipeline_trace.txt - Detailed trace log of all processes and their various metrics