Update README.md

README.md

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 ![ARETE Logo](assets/arete-logo-transparent.png)
 
-## Introduction
+## What is ARETE?
 
-**ARETE** is a bioinformatics best-practice analysis pipeline for AMR/VF LGT-focused bacterial genomics workflow.
+**ARETE** is a bioinformatics best-practice analysis pipeline for profiling the **genomic repertoire** and **evolutionary dynamics** of microorganisms with a particular focus on pathogens. We use ARETE is to identify important genes (e.g., those that confer antimicrobial resistance or contribute to virulence) and mobile genetic elements such as plasmids and genomic islands, and infer important routes by which these are transmitted using evidence from recombination, coevolution, and phylogenetic tree comparisons.
+
+ARETE produces a range of useful outputs, including those generated by each tool integrated into the pipeline, as well as summaries across the entire dataset such as phylogenetic profiles. Outputs from ARETE can also be fed into packages such as Coeus and MicroReact.
+
+ARETE has been applied to datasets ranging from fewer than ten to over 10,000 genomes from a multitude of species and genera including _Enterococcus faecium_, _Escherichia coli_, _Listeria_, and _Salmonella_. Although ARETE was primarily developed with pathogens in mind, inference of pan-genomes, mobilomes, and phylogenomic histories can be performed for any set of microbial genomes, with the proviso that reference databases are much more complete for some groups than others! The tools in ARETE work best at the species and genus level of relatedness.
+
+# Table of Contents
+1.[About the pipeline](#about)
+
+## About the pipeline <a name="about"></a>
 
 The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker / Singularity containers making installation trivial and results highly reproducible.
 Like other workflow languages it provides [useful features](https://www.nextflow.io/docs/latest/getstarted.html#modify-and-resume) like `-resume` to only rerun tasks that haven't already been completed (e.g., allowing editing of inputs/tasks and recovery from crashes without a full re-run).
 The [nf-core](https://nf-cor.re) project provided overall project template, pre-written software modules when available, and general best practice recommendations.
 
-## Pipeline summary
-
 Read processing:
 
 - Raw Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))