Overview
We link genetic variation to traits and trace population history, with rigorous control of confounding and relatedness.
Salient features
- Association testing with covariate and structure control
- Fine-mapping, polygenic risk and causal inference
- Reduced-representation sequencing (GBS, RAD, Pool-seq)
Analyses we offer
Population genetic analysis
Estimates diversity, differentiation and demographic history from genotype data and simulations.
Methods: plink-ng, msprime, scikit-allel.
GWAS
Tests millions of variants for association with a trait while controlling for ancestry and relatedness, and reports annotated loci.
Methods: regenie, plink-ng, ldsc.
GBS analysis
Processes genotyping-by-sequencing data into SNP matrices for diversity studies and breeding.
Methods: ipyrad, GB-eaSy, GBS.
Pool-seq analysis
Estimates allele frequencies and differentiation from pooled-sample sequencing.
Methods: grenedalf, poolSeq.
RAD-seq analysis
Assembles restriction-site associated reads into loci and calls SNPs across many individuals.
Methods: ipyrad, poolSeq.
Admixture & population structure
Infers ancestry components, mixing events and relationships between populations.
Methods: admixtools, AdmixTools.
Ancient DNA analysis
Handles damaged, low-coverage ancient DNA with authenticity checks and appropriate genotyping.
Methods: nf-core eager.
Fine-mapping & polygenic risk scores
Narrows association signals to likely causal variants and builds polygenic scores for risk prediction.
Methods: susieR, PRScs, PRSice.
Mendelian randomization
Uses genetic variants as instruments to test whether an exposure causally affects an outcome.
Methods: TwoSampleMR.
eQTL mapping
Links genetic variants to changes in gene expression across individuals or cell types.
Methods: tensorqtl.
What you receive
- A written report with methods, parameters and interpretation
- Processed data tables and publication-quality figures
- Scripts and settings so every result can be reproduced
Not sure which analysis fits your data? Contact us and we will advise.