Data release to partners

Our Plasmodium projects routinely release genotype data to partners. This page provides summary information about these partner data releases.

Email notifications

When a partner data release is ready, an email notification will be sent to the contact person(s) and designated study associates for all partner studies with data in that release.

The email notification will contain:

  • Summary information (e.g. # samples from # partner studies, # high-quality SNPs)
  • A brief description of noteworthy updates or changes since the last partner release
  • Links to access the data via the MalariaGEN website

Data release email notifications are sent from the data [at] malariagen.net email address via an email service provider, Adestra. To help ensure that you receive these emails, we suggest adding data [at] malariagen.net to your address book.

Who can access the data

Direct access will only be given to the partner study contact person and any additional study associates specifically designated by the contact person. If you wish to query or update the contact(s) for your study, please email us at data [at] malariagen.net.

Accessing your data

To access your data, you will need to log in to the MalariaGEN website and navigate to the relevant web tool, My Studies (to download data packages and process reports) or My Genotypes (to browse genotypes).

My Studies

http://lookseq.sanger.ac.uk/mystudies/

Once logged in, you will see a list of the partner studies that you have permission to access. Partner studies are listed by Study ID.

To begin, select one or more partner studies; a tabbed box will appear at the bottom of the page.

Data downloads are available under the ‘Downloads’ tab. There are typically three downloads included in each partner data release:

  • Genotyping data – This quality-filtered data package contains our catalogue of high-quality SNPs, genotype data for your samples at each high-quality SNP, and the sequence read counts that underpin these genotype calls. Currently, genotyping data can be downloaded as vcf files. Some historical data releases are available as tab-delimited files.
  • Process report – This document provides important information to assist investigators in understanding and using these data packages, including details about the genotyping methods used and their assumptions and limitations.
  • Read counts – This exploratory data package contains the full list of unfiltered, potential SNPs, identified by sequence read alignments and the read counts at the potential SNPs for each sample.

Links to raw data are available under the ‘Sample status’ tab:

  • Sequencing reads – This column provides the sample accessions and links to the sequence read data in the European Nucleotide Archive (ENA). Please note that ENA accessions can be present before the data is available on the ENA website.

My Genotypes

Once logged in, you can browse your sample genotypes.

http://lookseq.sanger.ac.uk/mygenotypes/

Contact us

If you have any question about data access or are having trouble viewing your data, please see email us at data [at] malariagen.net.