Pf8: an open dataset of Plasmodium falciparum genome variation in 33,325 worldwide samples

The Pf8 data release includes 33,325 parasite samples collected in 34 different countries in Africa, Asia, South America and Oceania. From these, 24,409 are high-quality samples with complete metadata. In total, we identified more than 12 million variant positions (SNPs and indels). This record includes metadata and drug-resistance inference for samples contributed to MalariaGEN. To encourage specialised analyses, we additionally include the genetic distance matrix (full and SNP-only versions), measures of sample clonality (Fws), copy number variation (CNV) calls, and drug resistance inferences and rules files. Sequence alignment and genomic variant files (CRAM and VCF files) are not included in this record but will are publicly available under project accession PRJEB96783 via ENA and EVA, respectively. Further information on files may be accessed in the Pf8_README.txt file. These data are available open access under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0). Publications using these data should acknowledge and cite the source of the data. For more information on MalariaGEN P. falciparum projects, please visit: https://www.malariagen.net/parasite-observatory/ The methods used to generate the data are described in detail in "Pf8: an open dataset of Plasmodium falciparum genome variation in 33,325 worldwide samples", MalariaGEN et al., 2025, DOI: 10.12688/wellcomeopenres.24031.1 Details of the files in this record: - Pf8_samples.txt : sample metadata file in tab-delimited format - Pf8_fws.tsv : Fws values in tab-delimited format - Pf8_mean_genotype_distance.npy: genetic distance matrix in numpy format - Pf8_mean_genotype_distance_snp_only.npy: genetic distance matrix generated from SNP-only callset, in numpy format - Pf8_cnv_calls.tsv: copy number variation calls in tab-delimited format - Pf8-cnv-diagnostic-plots.zip: zipped directory containing diagnostic plots of CNV regions for all samples in .png format - Pf8_tandem_duplication_breakpoints.tsv: breakpoint pairs used in tandem duplication CNV calling in tab-delimited format - Pf8_drug_resistance_marker_genotypes.tsv : drug resistance marker genotypes file in tab-delimited format - Pf8_inferred_resistance_status_classification.tsv : inferred resistance status classification file in tab-delimited format - Pf8_resistance_classification.pdf : rules used to create Pf_8_inferred_resistance_status_classification.tsv in PDF format - PlasmoDB-54-Pfalciparum3D7-Genome.fasta: a FASTA 3D7 reference file created from PlasmoDB's release 54 - PlasmoDB-55_Pfalciparum3D7.gff.gz: a gzipped GFF file created from PlasmoDB's release 55 - Pf8_README.txt: further details on the files contained within the Pf8 release