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Output file descriptions
The main results from Ellipsis can be found in the reports folder in the specified output directory. These reports contain summarised results for all included isolates, and each file is described below.
This report contains information about each isolate regarding the completeness of the genome, and how many predicted plasmids are present. Additionally, the sequence type of each isolate is listed here. Note that if you supplied the pipeline with assemblies lacking circularity status of each contig, the pipeline will not be able to predict the completeness of the genomes. STs predicted from reads and assemblies are listed here if you use either assembly workflows.
This is the most detailed report, where the results for each contig is listed. This includes prokka, resfinder, virulencefinder, plasmidfinder, and MOB-Suite results. Note that this file may be quite large when working with draft assemblies.
This file contains the results for each element (plasmid/chromosome) predicted by MOB-Suite. Each element may be represented by several contigs, especially when working with draft assemblies. Here, similar results are listed as in the contig reports, thus these two files may be similar when looking at complete assemblies.
This report list results from the mash analysis in MOB-Suite, as well as predicted mobility, predicted host range, and other.
These reports contain the detailed results for each hit in the respective databases.
When running either the hybrid assembly workflow with trimming or the illumina assembly workflow, one MultiQC report is generated before trimming and one after. If running the hybrid assembly workflow without trimming, one MultiQC report will be generated from the raw reads.
These reports contain presence-absence results from the ARIBA resistance- and virulence gene analysis on an isolate level. Here, a 1 means the gene is present and passed quality checks, a 1* means the gene was identified, but did not pass quality checks, and 0 means the gene was not identified. The R script that analyses the reports from ARIBA accepts certain flags, to quality check the results. These flags are given to describe certain factors regarding the analysis, such as if the local assembly of the gene in question was broken, or if the gene was incomplete. Therefore, a 1* in the result file should be interpreted with caution, as it may only have detected half a gene or a broken gene, or some other issue.