Bacterial and viral pan-genomes used for evalution of k-mer indexes
Veselý, Pavel; Břinda, Karel; Sladký, Ondřej;
Bacterial and viral pan-genomes used for evalution of k-mer indexes
This record contains the following three datasets: E. coli pan-genome, obtained as the union of the E. coli genomes from the 661k collection. S. pneumoniae pan-genome: 616 genomes, as provided in RASE DB S. pneumoniae (https://github.com/c2-d2/rase-db-spneumoniae-sparc/) SARS-CoV-2 pan-genome, downloaded from GISAID https://gisaid.org/ (access upon registration) on Jan 25, 2023 (GISAID version 2023/01/23, 14,682,066 genomes, 430 Gbp) We stored all the data sets in the form of simplitigs computed by ProphAsm. We used ProphAsm at version v0.1.1 as ‘prophasm -i {original} -o {preprocessed} -k {preprocessing-k}’ and we used k = 32 for SARS-CoV-2 and S. pneumoniae and k = 63 for E. coli (which requires ProphAsm2).
- French Institute for Research in Computer Science and Automation France
- ETH Zurich Switzerland
- Charles University Czech Republic
- Inria Rennes - Bretagne Atlantique Research Centre France
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