An open dataset of Plasmodium falciparum - v.7.0

Project: P. falciparum Community Project

Released on 8 Dec 2022

This page provides information about the Pf7 dataset which contains genome variation data on over 20,000 worldwide samples of Plasmodium falciparum. Details of the key publication will be included here once available.

This release contains details on contributing partner studies, sample metadata and key sample attributes inferred from genomic data, and genomic data including raw sequence reads. A descrption of the dataset can be found here

These data are available open access. Publications using these data should acknowledge and cite the source of the data using the following format: "This publication uses MalariaGEN data as described in ‘Pf7: an open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples . MalariaGEN et al, Wellcome Open Research 2023, 8:22 https://doi.org/10.12688/wellcomeopenres.18681.1.

8 Dec 2022

Study information

Details of the 82 contributing partner studies, including description, contact information and key people

Download study information

8 Dec 2022

Sample provenance and sequencing metadata

Sample information including partner study information, location and year of collection, ENA accession numbers, and QC information for 20,864 samples from 33 countries.

Download sample provenance and sequencing metadata

12 Dec 2022

Measure of complexity of infections

Characterisation of within-host diversity (FWS) for 16,203 QC pass samples.

Download measure of complexity of infections

12 Dec 2022

Drug resistance marker genotypes

Genotypes at known markers of drug resistance for 16,203 samples, containing amino acid and copy number genotypes at six loci: crt, dhfr, dhps, mdr1, kelch13, plasmepsin 2-3.

Download drug resistance marker genotypes

12 Dec 2022

Inferred resistance status classification

Classification of 16,203 QC pass samples into different types of resistance to 10 drugs or combinations of drugs and to RDT detection: chloroquine, pyrimethamine, sulfadoxine, mefloquine, artemisinin, piperaquine, sulfadoxine- pyrimethamine for treatment of uncomplicated malaria, sulfadoxine- pyrimethamine for intermittent preventive treatment in pregnancy, artesunate-mefloquine, dihydroartemisinin-piperaquine, hrp2 and hrp3 gene deletions.

Download Inferred resistance status classification

12 Dec 2022

Drug resistance markers to inferred resistance status

Details of the heuristics utilised to map genetic markers to resistance status classification

Download drug resistance markers to inferred resistance status

 

12 Dec 2022

CRT haplotypes

Full crt gene haplotypes for 16,203 QC pass samples. These are available at ftp://ngs.sanger.ac.uk/production/malaria/Resource/34/Pf7_crt_haplotypes.txt.

12 Dec 2022

CSP C-terminal haplotypes

Full csp C-terminal haplotypes for 16,203 QC pass samples plus 6 lab strains. These are available at ftp://ngs.sanger.ac.uk/production/malaria/Resource/34/Pf7_csp_c_terminal_haplotypes.txt.

12 Dec 2022

EBA175 calls

eba175 allelic type calls for 16,203 QC pass samples.

Download EBA175 calls

12 Dec 2022

Reference genome

The version of the 3D7 reference genome fasta file used for mapping. This is available at ftp://ngs.sanger.ac.uk/production/malaria/Resource/34/Pfalciparum.genome.fasta

12 Dec 2022

Annotation file

The version of the 3D7 reference annotation gff file used for genome annotations. This is available at ftp://ngs.sanger.ac.uk/production/malaria/Resource/34/
Pfalciparum_replace_Pf3D7_MIT_v3_with_Pf_M76611.gff.

12 Dec 2022

Genetic distances

Genetic distance matrix comparing all 20,864 samples. This is available at ftp://ngs.sanger.ac.uk/production/malaria/Resource/34/Pf7_genetic_distance_matrix.npy

12 Dec 2022

Short variants genotypes

Genotype calls on 10,145,661 SNPs and short indels in all 20,864 samples from 33 countries, available both as VCF (ftp://ngs.sanger.ac.uk/production/malaria/Resource/34/Pf7_vcf/) and zarr (ftp://ngs.sanger.ac.uk/production/malaria/Resource/34/Pf7.zarr.zip) files.

 

Release notes

README file describes in fine detail all the files included in the release, the format and interpretation of each column, and contains some tips and tricks for accessing genotype data in VCF and zarr files.

NOTE: You may need to download a free FTP client to access the FTP links.