Pf-HaploAtlas: an interactive web app for spatiotemporal analysis ofP. falciparumgenes

Abstract

Monitoring the genomic evolution ofPlasmodium falciparum- the most widespread and deadliest of the human-infecting malaria species - is critical for making decisions in response to changes in drug resistance, diagnostic test failures, and vaccine effectiveness. The MalariaGEN data resources are the world’s largest whole genome sequencing databases forPlasmodiumparasites. The size and complexity of such data is a barrier to many potential end users in both public health and academic research. A user-friendly method for accessing and interpreting data on the genetic variation ofP. falciparumwould greatly enable efforts in studying and controlling malaria. We developed Pf-HaploAtlas, a web application enabling exploration of genomic variation without requiring advanced technical expertise. The app provides analysis-ready data catalogues and visualisations of amino acid haplotypes for all 5,102 coreP. falciparumgenes. Pf-HaploAtlas facilitates comprehensive spatial and temporal analyses of genes and variants of interest by using data from 16,203 samples, from 33 countries, and spread between the years 1984 and 2018. The scope of Pf-HaploAtlas will expand with each new MalariaGENPlasmodiumdata release. Pf-HaploAtlas is available online for public use athttps://apps.malariagen.net/pf-haploatlas, which allows users to download the underlying amino acid haplotype data, and its source code is freely available on GitHub under the MIT licence athttps://github.com/malariagen/pf-haploatlas.