CurSa: scripts to curate metadata and sample genomes from GISAID for analysis and display in nextstrain and...

The coronavirus SARS-CoV-2 is the most sequenced pathogen ever, with several million genome copies deposited in the GISAID database. This large amount of genomic information poses non-trivial bioinformatic challenges for those interested in studying the evolution of SARS-CoV-2. One common problem when studying the phylogeny of the coronavirus in its geographical context is to count with accurate information of the location of the samples. However, this information is filled by hand by research groups all over the world and sometimes typos and inconsistencies are introduced in the metadata when submitting the sequences to GISAID. Correcting these errors is laborious and time-consuming. Here, we provide a suite of Perl scripts designated to facilitate the curation of this vital information and perform a random sampling of genome sequences if necessary. The scripts provided here can be used to curate geographic information in the metadata and sample the sequences from any country of interest to ease the preparation of files for Nextstrain and Microreact, thus accelerating evolutionary studies of this important pathogen. CurSa scripts are accessible via: https://github.com/luisdelaye/CurSa/.