Resources

Curated links for bioinformatics and breeding

A collection of useful tools, tutorials, and references. This is not exhaustive — just things I’ve found genuinely helpful.

TipSuggest a resource

Know of something that should be here? Let me know or open a PR.

Learning Bioinformatics

General

• Bioinformatics Data Skills — Vince Buffalo’s excellent book on practical skills
• Rosalind — Learn bioinformatics through problem solving
• Harvard Chan Bioinformatics Core Training — High-quality free workshops

R for Genomics

• R for Data Science — Foundation for any R work
• Bioconductor — Core packages for genomic analysis
• vcfR documentation — The resource that inspired this site

Python for Genomics

• Biopython Tutorial
• scikit-allel — Population genetics in Python

Command Line & HPC

• Software Carpentry: Shell
• HPC Carpentry

Variant Calling & Quality Control

Tools

Tool	Purpose	Link
bcftools	VCF/BCF manipulation	samtools.github.io/bcftools
GATK	Variant discovery	gatk.broadinstitute.org
VCFtools	VCF filtering/stats	vcftools.github.io
Plink	GWAS, population genetics	cog-genomics.org/plink

Tutorials

• GATK Best Practices
• VCF format specification

Genomic Selection & Breeding

Software

Tool	Purpose	Link
BLUPF90	Genetic evaluation	nce.ads.uga.edu/html/projects/programs/
rrBLUP	Ridge regression BLUP	CRAN
BGLR	Bayesian regression	CRAN
sommer	GWAS & GS	CRAN
AlphaSimR	Breeding simulations	CRAN

Reading

• Meuwissen, Hayes & Goddard (2001) — The original genomic selection paper
• Genomic Selection in Animals and Plants

Population Genetics

Tools

Tool	Purpose	Link
ADMIXTURE	Ancestry estimation	dalexander.github.io/admixture
STRUCTURE	Population structure	web.stanford.edu/group/pritchardlab/structure.html
fastSTRUCTURE	Fast STRUCTURE	rajanil.github.io/fastStructure
PopGenome	R package	CRAN

Tutorials

• Population Genetics in R
• adegenet tutorials

Data Visualization

R Packages

• ggplot2 — Grammar of graphics
• plotly — Interactive plots
• ComplexHeatmap — Publication-quality heatmaps
• CMplot — Manhattan and QQ plots

Color Palettes

• viridis — Colorblind-friendly palettes
• RColorBrewer — Classic palettes
• Coolors — Color scheme generator

Databases & Data Sources

Reference Genomes

• Ensembl
• NCBI Genome
• Phytozome (plants)

Variant Databases

• dbSNP
• EVA — European Variation Archive
• ClinVar (human clinical variants)

Breeding/Agricultural

• GRIN — USDA germplasm
• Breedbase — Breeding database platform
• DeltaBreed — Breeding Insight data management platform

Reproducibility & Workflows

Workflow Managers

• Nextflow — Popular for bioinformatics
• Snakemake — Python-based
• targets — R pipelines

Containers

• Docker
• Singularity/Apptainer — HPC-friendly
• BioContainers — Pre-built bioinformatics containers

Documentation

• Quarto — What this site is built with
• MkDocs Material

Communities

• Biostars — Bioinformatics Q&A
• SEQanswers
• r/bioinformatics
• Bioconductor Slack

---

Last updated: January 2025