Genotyping of European Toxoplasma gondii strains by a new high-resolution next-generation sequencing-based method

The data set comprises 164 FASTQ files generated with an Ion AmpliSeq-based genotyping method for Toxoplasma gondii and a BED file used for the design of the Ion AmpliSeq primer panel. The FASTA file named as "AmpliSeq-ME49-Reference" was used as a reference for mapping and data analysis of the FASTQ files. The GZ file named as "Tgondii_IonAmpliSeq_Results_SNPs_VCF" is a VCF file, which contains all SNPs identified within the 164 FASTQ files relative to the AmpliSeq-ME49-Reference. The VCF file was converted into a FASTA file named as "Tgondii_IonAmpliSeq_Results_SNPs", which also contains the SNPs identified within the 164 FASTQ files relative to the AmpliSeq-ME49-Reference. The work is published in the European Journal of Clinical Microbiology & Infectious Diseases with the title "Genotyping of European Toxoplasma gondii strains by a new high‑resolution next‑generation sequencing‑based method"; https://doi.org/10.1007/s10096-023-04721-7