A pipeline to use Lep-Map3 to create linkage maps and LepAnchor for anchoring and orienting genome assemblies with said linkage maps.

A collection of WDL bioinformatic workflows to benchmark markers coming from different pipelines using linkage map quality as a diagnosis.

Repository of SmoothDescent R package. Smooth Descent is a map-cleaning algorithm that can calculate identity by descent probabilities and correct genotyping errors based on marker maps.

An R package to visualize genetic maps.

VCF to JoinMap loc (variant-to-marker) conversion tool

A Shiny web application that wraps the 'onemap' R package to let users perform linkage mapping and QTL visualisation on biparental mapping populations (F2 intercross and backcross) without writing any code.

Genetic mapping and QTL analysis of basil

Analyses of my MSc Thesis: "Genetic architecture of parasitoid counteradaptation to symbiont-conferred resistance"

Marmorata Linkage Map

A Python wrapper and standalone library for MSTmap and its web-server https://mstmap.org

This program leverages zero recombination clusters and their relative positions on a linkage group to impute phases for missing data with high fidelity.

Converts between linkage output formats {Genehunter, Merlin, Simwalk, Swiftlink} → Allegro