Welcome to CorGAT’s documentation!

CorGAT is a collection of Perl utilities that can be used to align complete assemblies of SARS-CoV-2 genomes wih the reference genomic sequence, to obtain a list of polymorphic positions and to annotate genetic variants according to the method described in Chiara et al 2020 to be published soon (hopefully). The manuscript is currently submitted and undergoing peer review.

This software package is composed of 2 very simple scripts and a collection of files with functional annotation data. Since the number of available SARS-CoV-2 genomic sequences is increasingly constantly, these files are regularly updated on a monthly basis. If you do not feel comfortable in installing/running CorGAT from the command line, you can find a Galaxy running the software at http://corgat.ba.infn.it/galaxy , or download a dockerized version of the Galaxy, with all the tools here.


If you find any of this software useful for your work, please cite:

Chiara M, Horner DS, Gissi C, Pesole G. Comparative genomics provides an operational classification system and reveals early emergence and biased spatio-temporal distribution of SARS-CoV-2 bioRxiv 2020.06.26.172924; doi: https://doi.org/10.1101/2020.06.26.172924


Chiara M, Zambelli F, Tangaro MA, Mandreoli P, Horner DS, Pesole G. CorGAT: a tool for the functional annotation of SARS-CoV-2 genomes. Under Peer review

If you find any issue with the software, please contact me, or report it on github.

Indices and tables