David Lougheed

Software & Projects

Featured

• STRkit

  STRkit is a short tandem repeat (STR) genotyper for long read sequencing data such as PacBio HiFi. This tool was originally created as part of my Master's degree in Human Genetics at McGill, and is described in a journal article in Genome Research (Lougheed et al. 2026).

  
• SNIPe

  A web tool for optimally choosing environmental DNA (eDNA) primer pairs to identify a set of taxa. Part of a publication by Tournayre et al. (2024).

  
• Bento

  A platform for storing, analyzing, and visualizing genomic and epigenomic data, created while working at the Canadian Centre for Computational Genomics (C3G). Many people have worked on this platform, not just myself!

  
• EpiVar Browser

  A browser for exploring quantitative trait loci and their associations with genotype and ancestry. Published as a Bioinformatics application note: Lougheed et al. (2024), and as part of a publication by Aracena et al. (2024). Many people have worked on this browser, and much of it was written by Romain Grégoire, a previous member of C3G.

Other

• TeloScore

  A small similarity scoring tool for human telomere alleles using the output of the Telogator2 tool, created for work done by PhD student Yuxin Zhou in Prof. Guillaume Bourque's lab.

• David's Trail Guide System

  A set of three components for creating mobile trail guide applications: a content server with a corresponding front-end and a white-label Expo application. I used this to build the latest version of the Elbow Lake Trail Guide.

  
• MHCut Browser (2019)

  A browser for microhomologies at variant CRISPR/Cas9 cut sites. Part of a publication by Grajcarek et al. (2019).

• Elbow Lake Trail Guide

  An interactive trail guide app available on Android and iOS.

• Canadian Field Stations (2014-2016; 2024)

  A compendium of field stations across Canada which I assist in maintaining.