insapathogenomics/reportree repository overview

⁠ReporTree

Genomics-informed pathogen surveillance strengthens public health decision-making, thus playing an important role in infectious diseases’ prevention and control. A pivotal outcome of genomics surveillance is the identification of pathogen genetic clusters/lineages and their characterization in terms of geotemporal spread or linkage to clinical and demographic data. This task usually relies on the visual exploration of (large) phylogenetic trees (e.g. Minimum Spanning Trees (MST) for bacteria or rooted SNP-based trees for viruses). As this may be a non-trivial, non-reproducible and time consuming task, we developed ReporTree, a flexible pipeline that facilitates the detection of genetic clusters and their linkage to epidemiological data.

ReporTree can help you to:

• obtain genetic clusters at any threshold level(s) of a tree, SNP or cg/wgMLST allele matrix, VCF files, sequence alignment, or distance matrix
• obtain summary reports with the statistics/trends (e.g., timespan, location, cluster/group composition, age distribution etc.) for the derived genetic clusters or for any other provided grouping variable (e.g., clade, lineage, ST, vaccination status, etc.)
• obtain count/frequency matrices for the derived genetic clusters or for any other provided grouping variable
• identify regions of cluster stability (i.e., threshold ranges in which cluster composition is similar), a key step for nomenclature design
• maintain cluster nomenclature between runs and generate hierarchical codes at your levels of interest

In summary, ReporTree facilitates and accelerates the production of surveillance-oriented reports, thus contributing to a sustainable and efficient public health genomics-informed pathogen surveillance.

Check the GitHub page for details in ReporTree usage: https://github.com/insapathogenomics/ReporTree⁠