DATA ANALYSIS

UCSF

Tools, resources and protocols developed  to understanding complex infectious disease dynamics. Includes:

• MAD4HatTeR
• dcifer
• moire
• THEREALMcCOIL
• flexfit
• MicroSPAT

Broad Institute

See also:
AmpSeQC: Amplicon sequencing and quality control pipeline
paneljudge: R package to judge the performance of a panel of genetic markers using simulated data

LSHTM

A pipeline which allows users to analyse Plasmodium malaria whole genome sequencing data to predict species and potential drug resistance

Harvard T.H. Chan School of Public Health (HSPH)

MalKinID (Malaria Kinship Identifier) is a likelihood-based classification model designed to identify genealogical relationships among malaria parasites based on genome-wide IBD proportions and IBD segment distributions. 

Brown University

MIPTools is a suite of computational tools that are used for molecular inversion probe design, data processing, and analysis.

MalariaGEN

Open source tools to enable researchers around the world to access and analyse mosquito genome variation data.
See the vector data user guide and the Malaria Vector Genome Observatory page.

MalariaGEN

Widely accessible data-driven applications to support and accelerate the use of genomic surveillance data by malaria control programs and policymakers.
See the parasite data user guide.

University of Massachusetts Medical School (UMass)

Local haplotype assembler designed for complex infections and highly variable genomic regions with poor reference mapping

Imperial College London

Interactive web-based App that can be used to design a pfhrp2/3 deletion study and to analyse the results of such a study

MalariaGEN

This App enables any user with an internet connection to study and track genetic mutations across any gene in the P. falciparum core genome.

Community-driven platform designed to simplify Plasmodium Genomic Epidemiology analysis. Includes sections on:

• • Data
  • Tool Landscaping
  • Software Standards
  • Tutorials

Brown University

Intended for use on targeted amplicon sequencing data for haplotype frequency estimation for multiple samples from a population (link)

Broad Insitute

Terra is a secure cloud-based data platform enabling pathogen genomic data analysis in public health, clinical, and academic settings. Malaria Resources on Terra is a community hub that enables both private and collaborative data analysis.