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Malaria Vector Genome Observatory

Data for Anopheles mosquito research, surveillance and control.

Data Training API Compute Partners Research

How is malaria being transmitted?

We need a better understanding of which Anopheles mosquito species are transmitting malaria in different places, and how this is changing in response to interventions, urbanisation and climate change.

Where is insecticide resistance evolving and spreading?

Insecticide resistance is the biggest threat to our current tools for mosquito control. When resistance emerges, we need to identify and characterise it quickly, assess the risk, and track it as it spreads.

How can we move beyond control towards elimination?

Our current tools for mosquito control will only take us so far. We need to invent new ways to stop mosquitoes transmitting malaria, and be smart in how we use them.

The observatory is a collaborative effort to sequence the genomes of thousands of Anopheles mosquitoes and use those data to improve malaria control.

The observatory at a glance


Data

Access carefully-curated genomic data which has been optimised for analysis in the cloud.

Training

Learn how to analyse data in the observatory through our hands-on online training course.

API

Use our open source Python package to explore, visualise and analyse data interactively.

Compute

Access free cloud computing services to analyse data wherever you are.

Partners

Scientists and engineers from around the globe are contributing samples, data and expertise to help build the observatory.

Research

Data from the observatory are powering new research into vector biology and control.

Data

Access data from whole-genome sequencing of Anopheles mosquitoes collected from natural populations in countries affected by malaria.


Anopheles gambiae complex

20,935 genomes from 31 countries

Anopheles funestus subgroup

3,231 genomes from 16 countries

Anopheles minimus

302 genomes from 1 country

Training

Learn about the biology, technology, data and analytical methods involved in genomic surveillance of Anopheles mosquitoes.

Zoom screen with participants of the PAMCA-MalariaGEN training course

Video lectures in French or English and notebooks with executable code examples.

Study at your own pace, or enroll in an online course to learn alongside others with support from experienced teaching assistants.

Visit training course website

API

Our cloud-native software for Python supports a range of functions for data access, visualisation, and statistical analysis.

Explore available samples by country of origin, collection date and taxon.

Explore available samples by collection location.

Compute frequencies of genetic variants in genes of interest.

Compare the frequency of genetic variants between different geographical areas.

Analyse changes in variant frequencies over time.

Browse sequence read alignments and assess the evidence for genetic variation in individual samples.

Visualise sequence read coverage and evidence for copy number variation in individual samples.

Visualize and compare copy number variation in multiple samples.

Explore population structure with principal components analysis.

Investigate hybridisation and introgression between species with ancestry-informative markers.

Quantify and compare genetic diversity between populations.

Infer runs of homozygosity and investigate evidence for inbreeding.

Perform genome-wide selection scans to discover new resistance genes.

Find genes where adaptive gene flow is occurring between countries or species.

Use haplotype clustering to investigate selective sweeps and gene flow within a gene of interest.

Use haplotype networks to explore selective sweeps and gene flow within a gene of interest.

Compute

Run your analysis in the cloud using these computing services.


Google Colab

Colab is an interactive computing service provided for free by Google Research and is ideal for exploratory analyses.

MalariaGEN Datalab

The Genomic Surveillance Unit at the Sanger Institute hosts a JupyterHub service running in Google Cloud that is available for free to observatory partners for more intensive analyses.

Terra

Terra is a cloud platform for biomedical research supporting workflows and interactive notebooks, and can be used for a wide range of analyses.

Alternatively, observatory data can be downloaded to your own compute resources to run analyses locally.

Partners

Groups and individuals from around the world have contributed biological samples, sequencing capacity, computational resources, time and expertise to build the observatory.


The Pan-African Mosquito Control Association (PAMCA) Anopheles Genomics programme is working to build capacity for malaria vector genomics across Africa.
The Genomics for African Anopheles Resistance (GAARD) project aims to identify new genes and regulatory regions associated with insecticide resistance.
Target Malaria is developing innovative approaches to reduce the population of malaria-transmitting mosquitoes in sub-Saharan Africa.
The PAMGEN project is researching genetic interactions between malaria parasites, vectors and human communities across different African environments.

Research

The observatory is powering new research into the biology and control of malaria vectors.


May 31, 2024
Variation in spatial population structure in the Anopheles gambiae species complex
May 30, 2024
A metagenomic analysis of the phase 2 Anopheles gambiae 1000 genomes dataset reveals a wide diversity of cobionts associated with field collected mosquitoes
May 29, 2024
Discovery of knock-down resistance in the major African malaria vector Anopheles funestus
May 15, 2024
AnoPrimer: Primer Design in malaria vectors informed by range-wide genomic variation
April 26, 2024
The Anopheles coluzzii range extends into Kenya: detection, insecticide resistance profiles and population genetic structure in relation to conspecific populations in West and Central Africa
March 18, 2024
Speciation within the Anopheles gambiae complex: high-throughput whole genome sequencing reveals evidence of a putative new cryptic taxon in 'far-west' Africa
March 14, 2024
Cryptic population structure and insecticide resistance in Anopheles gambiae from the southern Democratic Republic of Congo
March 13, 2024
Copy number variants underlie the major selective sweeps in insecticide resistance genes in Anopheles arabiensis from Tanzania
March 01, 2024
Evaluating evidence for co-geography in the Anopheles–Plasmodium host-parasite system
February 14, 2024
Genomic Profiling of Insecticide Resistance in Malaria Vectors: Insights into Molecular Mechanisms
February 01, 2024
Parallel evolution in mosquito vectors – a duplicated esterase locus is associated with resistance to pirimiphos-methyl in An. gambiae
November 25, 2023
Whole-genome sequencing of major malaria vectors revealed an evolution of new insecticide resistance variants in a longitudinal study in Burkina Faso
November 22, 2023
Mechanisms of transcriptional regulation in Anopheles gambiae revealed by allele specific expression
August 16, 2023
Genome-wide association studies reveal novel loci associated with pyrethroid and organophosphate resistance in Anopheles gambiae and Anopheles coluzzii
July 19, 2023
Mitochondrial variation in Anopheles gambiae and An. coluzzii: phylogeographic legacy of species isolation and mito-nuclear associations with metabolic resistance to pathogens and insecticides
April 13, 2023
Dispersal inference from population genetic variation using a convolutional neural network
February 06, 2023
Single nucleotide polymorphism (SNP) in the doublesex (dsx) gene splice sites and relevance for its alternative splicing in the malaria vector Anopheles gambiae
January 25, 2023
RNA-Seq-Pop: Exploiting the sequence in RNA-Seq - a Snakemake workflow reveals patterns of insecticide resistance in the malaria vector Anopheles gambiae
November 28, 2022
Population genomics reveal distinct and diverging populations of An. minimus in Cambodia
November 13, 2022
Analysis of the Genetic Variation of the Fruitless Gene within the Anopheles gambiae (Diptera: Culicidae) Complex Populations in Africa
May 25, 2021
Genetic variation at the Cyp6m2 putative insecticide resistance locus in Anopheles gambiae and Anopheles coluzzii
May 05, 2021
Contemporary Ne estimation using temporally spaced data with linked loci
March 09, 2021
Discovery of Ongoing Selective Sweeps within Anopheles Mosquito Populations Using Deep Learning
February 16, 2021
The genetic architecture of target-site resistance to pyrethroid insecticides in the African malaria vectors Anopheles gambiae and Anopheles coluzzii
February 15, 2021
Novel genotyping approaches to easily detect genomic admixture between the major Afrotropical malaria vector species, Anopheles coluzzii and An. gambiae
January 21, 2021
Resistance to pirimiphos-methyl in West African Anopheles is spreading via duplication and introgression of the Ace1 locus.
October 01, 2020
Evolution of the Insecticide Target Rdl in African Anopheles Is Driven by Interspecific and Interkaryotypic Introgression
September 28, 2020
Genome variation and population structure among 1142 mosquitoes of the African malaria vector species Anopheles gambiae and Anopheles coluzzii
August 01, 2019
Whole-genome sequencing reveals high complexity of copy number variation at insecticide resistance loci in malaria mosquitoes
April 09, 2019
Robust Estimation of Recent Effective Population Size from Number of Independent Origins in Soft Sweeps
November 29, 2017
Genetic diversity of the African malaria vector Anopheles gambiae
June 23, 2017
Panoptes: web-based exploration of large scale genome variation data
June 25, 2014
Adaptive introgression between Anopheles sibling species eliminates a major genomic island but not reproductive isolation