Reportree
Introduction
Reportree, similarly to GrapeTree, buidls tree-graphs of distance for microorganisms, starting from allelic profiles of the samples. The tree is built using the "Minimum Spanning Tree" (MSTree or MST) algorithm.
Once the tree has been calculated, it can be visualized directly in Cohesive (using GrapeTree) through the integrated system for tree visualization, available in the completed analysis' summary.
Run Analysis Reportree
The analysis Reportree can be selected from the run analyses page.
The input selection UI delivers an advanced input selection mode, to allow selection of all types of supported input files at once.
Accepted inputs are:
For all possible inputs, is imperative that the program used to calulate allelic profiles is chewBBACA, so please mind the selected software, when launching 4TY_cgMLST or 4TY_wgMLST, if you wish to run GrapeTree later on.
It will be necessary to specify the 4TY_cgMLST__chewbbaca schema for the appropriate species (selection available in the parameter section), if the selected input consists of cgMLST allelic profiles. The field is pre-filled with the most appropriate schema for the microorganism matching the codes of samples in the cart or tag used for requesting the analysis.
A link to Check analysis will be created after launching the requested analysis. The system will notify the user after a succesful analysis launch and once execution has ended.
The analysis summary lists the output directory and additional options, such as access to some of the metadata, log and output files and direct graph visualization (both MSTree and NJ graphs) thanks to GrapeTree's integration in Cohesive.
Output directory
Please refer to Cohesive's specific Wiki page for information on file download.
The output directory is available at the link in the download page or at the link in the analysis' summary card. The results directory is located directly in the root directory. Inside results there are 2 subdirectories:
- meta: ("metadata") contains log and configuration files.
- result: contains the analysis' output files.
The following table lists output files stored in results.
| File | Description | Location |
|---|---|---|
| cgMLST.tsv | tsv table with alleles identified by chewBBACA during cgMLST. Rows: samples; Columns: loci. | cartella result |
| missing_loci.tsv | list of loci not shared between samples, thus discarded because uninformative for tree construction | cartella result |
| reportree.dist | summary text file with Reportree's caculated distances | cartella result |
| reportree.mx | table with samples' relative distance matrix | cartella result |
| reportree.nw | nwk (newick) treefile obtained with MSTree algorithm | cartella result |
| reportree_ST_iso_year_count_matrix.tsv | tsv table with Sequence Type (ST) quantities by year | cartella result |
| reportree_ST_iso_year_freq_matrix.tsv | tsv table with Sequence Type (ST) frequencies by year | cartella result |
| reportree_ST_summary.tsv | summary table of STs and metadata | cartella result |
| reportree_clusterComposition.tsv | tsv table of info on sample clusters | cartella result |
| reportree_iso_year_summary.tsv | summary table of ST percentages and origin by year | cartella result |
| reportree_metadata.tsv | sample metadata tsv table | cartella result |
| reportree_metadata_w_partitions.tsv | sample metadata tsv table with cluster info | cartella result |
| reportree_metrics.tsv | Reportree cluster metrics | cartella result |
| reportree_partitions.tsv | tsv table of cluster subdivision | cartella result |
| reportree_partitions_summary.tsv | tsv summary table of STs with metadata and cluster info | cartella result |
| reportree_puntoprelievo_summary.tsv | tsv summary table of STs by origin | cartella result |
| reportree_stableRegions.tsv | Wallace coefficient Stability Regions | cartella result |
nwk files contain all of the tree's data and can be visualized through GrapeTree or an external tree-graph visualization software.
