Welcome to the webserver of Malaria-Profiler - a pipeline which allows users to analyse Plasmodium malaria whole genome sequencing data to predict species and potential drug resistance. Follow the instructions below to upload a new sample or view analysed runs.

How does it work?

The pipeline searches for small variants (SNPs and indels) in genes associated with drug resistance. It will also report the species and geographical location. By default it uses Trimmomatic to trim the reads, BWA (or minimap2 for nanopore) to align to the reference genome and freebayes to call variants.

Upload your samples

Step 1 - Profile your sample

Upload your next generation sequencing data in fastq or bam format. When you upload your data, the run will be be assigned a unique Result ID.

Step 2 - View the results

If you have run analysis before, find your results by entering your unique Result ID into the search box.


Species, resistance and geographical region is predicted using the curated Plasmodium database. This database has been tested using over 10,000 samples with genotypic data. You can read more about the markers present in the library at the time of testing here or you can take a look at the up to date CSV file here.

If you have access to a linux or osX operating system then you can download the commandline version of Malaria-Profiler. For more information on this please visit the github repository.

We are always looking to improve Malaria-Profiler. If you see some results that don't look right or would like to see some additional functionality in the future, don't hesitate to get in touch via the section on our GitHub page.

Phelan, J. E. et al. in press