The following custom python scripts were using for developing the seventh pandemic MGT.
Script 1: Identifies core genes that are paralogous and orthologous split into multiple fragments by erroneous assemble and/or annotation.
Script 2: Determines the quality of allele assembly for each core gene.
Script 3: Identifies core genes that contain homopolymer tracts of eight of more bases in length.
Script 4: Creates multiple sequence alignment for a core gene. Output is further used in dN/dS calculation.
Script 5: Assigns core genes into MGT levels based on a multifactorial preference system. Genes are organised depending on minimum distance of separation, selection pressure and reliability.
insilico-genotyper: A blast-based algorithm for in-silico typing of V. cholerae genomes.