 Welcome everybody, I'm Erika Ferrandi and I'm a research fellow at the Institute of Biomembranes, Biologetics and Molecular Biotechnologies of Bari, in Italy, and I'm currently working at the Department of Biosciences of the University of Milan. The timely and rapid tracking of novicescope to variants and mutations is a priority in the fight against the pandemic, especially as these mutations or variants may become a source of concern for national and international health authorities. Here we present Korgat and Korgat Tracker, a complete set of tools for the functional annotation of SARS-CoV-2 genomes and for tracking mutations and variants of concern in space and time. Korgat, or the coronavirus genome analysis tool, is a collection of per-utilities and annotation files, which are used to perform the functional annotation of SARS-CoV-2 genetic variants. At the bottom of this slide you can see preview of the on-page of the galaxy version of the tool. Briefly, Korgat allows to align complete assemblies of SARS-CoV-2 genomes to the reference genomic sequence in order to obtain a list of polymorphic regions, which are then used to annotate a genetic variant. The output of the tool consists of the simple table, which contains the functional notation of the genetic variants previously identified, and also a series of additional information, all listed at the top of this slide. It is important to underline that information highlighted in orange, both in the list and in the example output picture, are all unique to Korgat derived functional annotations. Korgat Tracker is a shiny-based dashboard that allows the visualization of the prevalence of SARS-CoV-2 lineages and mutations of concern as annotated by Korgat. The galaxy release of this tool is currently under development. In Korgat Tracker, data are represented in an interactive way, and the user can personalize several visualization parameters by the means of a set of widgets. All the parameters that can be personalized are listed at the bottom of the slide, and here you have an overview of all the widgets available to personalized data visualization. Korgat Tracker produces three different kinds of plots. More in detail, we have a set of bar plots that represent the number of occurrences of lineages and mutations on a weekly basis. Then we have a set of pictures showing the cumulative prevalence of SARS-CoV-2 lineages and mutations, and last but not least, we have a set of scatter plots representing the number of weekly occurrences for user-selective lineage or mutation. Furthermore, to enable a more efficient tracking of emerging lineages in Korgat Tracker, lineage annotations can be kind of augmented by reporting the list of mutations of concern that are observed in a genome, but that are not specific to its assigned lineage. These augmented annotations are called lineages plus in app, and their prevalence in time is represented through a bar plot and the part chart, as you can see in the pictures reported. Overall, we believe that Korgat and Korgat Tracker will provide a useful addition to the currently available arsenal of bioinformatics methods and tools for the genomic surveillance of SARS-CoV-2. Korgat, in fact, has a sensitivity which is comparable to other tools with a similar function. However, it also provides an additional layer of information. For example, thanks to the application of our set of tools, we were able to identify a collection of Italy-specific misclassified SARS-CoV-2 genomes. More in detail, these genomes were classified as B1 by classical SARS-CoV-2 annotation methods. However, our system highlighted how they presented additional mutations in the spike protein, as you can see from the reported bar plot. More in depth analysis allowed us to observe that these genomes shared a consistent proportion of the mutations with B1 lineages, but they still present a group-specific mutation, more specifically P681H mutation on the spike protein. It is possible at this point to speculate that these genomes represent the newly immersed lineage. However, further investigations are required to verify these hypotheses. Finally, it is recent news that P1 plus P681H lineages were recently added by the ACDC to the list of variants under monitoring. Regarding the availability of the tools, again, Korgat is already available to Galaxy, whereas the Galaxy release for Korgat tracker is under development. Furthermore, additional information about the single tools, their code, and their functioning in detail can be found in the corresponding GitHub repository. All the useful links for the availability of the tool here presented are reported in this slide. To conclude, I want to thank my supervisor, Dr. Matteo Chiara, all the co-authors and people working on this project and all of you who are listening. Thank you.