SwarmGenomics

SwarmGenomics

A unified pipeline and data portal for individual‑based whole‑genome analyses.

Browse Data Teaching Slides Explore GitHub Repo bioRxiv PDF

About

SwarmGenomics is a modular pipeline for reference‑based genome assembly and individual‑based genetic analyses (e.g. heterozygosity, runs of homozygosity, PSMC, repeat analysis, mitogenome assembly, NUMTs). This site serves as the course & data portal.

SwarmGenomics overview

What’s on this site

  • Explore — interactive data analysis of the comparative dataset from the paper. Choose X/Y variables, color by Class or a numeric variable, apply log scales, add a regression line (with r and p), and optionally highlight a species. Open: explore.html.
  • GitHub — direct link to the SwarmGenomics repository with code, pipeline scripts and documentation. Open: GitHub Repo.
  • Data — downloads for the datasets used in the paper, including BAMs, reference genomes, and all‑sites VCFs for all species analyses. Open: data.html.
  • Teaching — slide decks that are free to use to run your own SwarmGenomics course. Open: teaching_slides.html.

Further reading