Recently I started using Panseq (literally yesterday), recommended by a fellow Biostars user, and I have some questions about the output files.
- The file "binary_table.txt" shows the presence/absence of the pan-genome among all genomes in the queryDirectory. So if I choose only genomic fragments that all strains analysed have a "1", theoretically I am choosing only genomic regions from the "core" genome, right?
- The file "coreGenomeFragments.fasta" shows all pan-genome fragments that are considere "core". But, I have manually checked a few sequences, and some of them were different in some strains. Can I alter the configuration file so that Panseq only chooses sequences that have a 100% match between all strains? (i.e. altering the values of "percentIdentityCutoff" and "coreGenomeThreshold", which I have used the default values in the first test run).
Many thanks in advance!