GENOMICS 30 days · 6 modules · Online

RAD-Seq Population Genetics Workshop (30-Day, Online)

Demultiplex restriction site reads, build loci, call SNPs, and study genetic variation and population structure.

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About this workshop

RAD-Seq sequences only the DNA next to restriction-enzyme cut sites, which makes it a cost-effective way to find thousands of genetic markers across many individuals. That has made it popular for population genetics, linkage maps and studies of species with no genome. This workshop covers the whole analysis: understanding how the enzymes shape the data, separating reads by individual using barcodes, cleaning reads, and building loci with or without a reference genome. You then call SNPs, filter genotypes for depth, missing data and artefacts, and export the results for downstream tools. The final modules show how to measure diversity, visualise population structure with PCA and compare populations, so you can move from raw reads to a population-level result.

Tools and pipelines you will use

This workshop emphasizes standard, open-source bioinformatics tools widely used in peer-reviewed genomics literature:

Stacks ↗Bowtie2 ↗BCFtools ↗VCFtools ↗PLINK ↗fastSTRUCTURE ↗

What you will learn

Module 1 Foundations
Week 1
Linux and command-line basics Run tools and manage files.
RAD-Seq principle How restriction enzymes reduce the genome.
Experimental design Enzymes, sample numbers and depth.
Read quality control Check and clean reads.
Module 2 Demultiplexing and cleaning
Barcodes Separate reads by individual.
Trimming and filtering Remove low-quality and short reads.
Recovering reads Handle errors in barcodes and cut sites.
Sample summary Report reads per individual.
Module 3 Locus construction
With a reference genome Align reads and build loci.
Without a reference genome Cluster reads into de novo loci.
Parameter choices Understand settings that change locus numbers.
Locus quality Check coverage and missing data.
Module 4 SNP discovery
Calling SNPs Identify variants across individuals.
Genotype filtering Apply depth, missing-data and frequency filters.
Removing paralogs and artefacts Reduce false variants.
Output formats Export data for downstream tools.
Module 5 Population analysis
Diversity measures Compute heterozygosity and related statistics.
Population structure Use PCA and clustering to see groups.
Differentiation Compare populations with FST.
Visualization Plot results for presentation.
Module 6 Mini-project and report
Week 4
Project dataset Analyse a public RAD-Seq dataset.
Reproducible workflow Record every step and setting.
Figures and write-up Present structure and diversity results.
Review and next steps Discuss design improvements.

What you receive & prerequisites

What you receive

  • 30 days of structured online self-paced access & mentor guidance
  • Curated real-world NGS benchmark datasets
  • Reusable pipeline scripts and command-line code templates
  • Independent capstone mini-project evaluation
  • Certificate of Completion issued by Xenoi Biotech Pvt. Ltd.

Prerequisites & setup

  • Basic life science background (B.Sc., M.Sc., B.Tech, or research scholar)
  • No prior programming or Linux experience required (covered in Module 1)
  • Laptop or PC with 8 GB RAM and internet access
  • Remote compute setup instructions provided during onboarding

Course curriculum designed by Anjali Chaudhary, Bioinformatics Scientist at Xenoi Biotech.

Last updated: October 2026

Related workshops & services

Broaden your computational biology expertise with complementary workshops:

Need this analysis done for your laboratory data? Explore our Genomics Services or consult on Custom Bioinformatics Pipelines.

Frequently asked questions

Is this RAD-Seq workshop delivered online?

Yes. All Xenoi Biotech workshops are delivered 100% online, allowing researchers and students across India and internationally to participate with remote compute support.

How long is the workshop and what is the workload?

The workshop runs for 30 days across 6 structured modules. Learners typically dedicate 1 to 2 flexible hours per day to work through pipeline commands, code exercises, and the mini-project.

Who is this workshop designed for?

It is built for B.Sc., M.Sc., and Ph.D. students, postdoctoral researchers, faculty members, and industry professionals in biotechnology, biochemistry, microbiology, and medicine who need to analyze NGS datasets independently.

What will I learn in this workshop?

You will learn Stacks pipeline execution (process_radtags, ustacks/pstacks, cstacks, sstacks, populations), SNP filtering for call rate and minor allele frequency, Fst differentiation, heterozygosity metrics, PCA, and ancestry clustering.

What are the fees, dates, and enrollment details?

The workshop fee is MRP ₹5,000, inclusive of GST. Batch dates are shared on enquiry. Use the Enrol now button to reserve your place or receive the upcoming schedule.

Fees, dates and batches

The workshop fee is MRP ₹5,000 (incl. GST). Batch dates and onboarding materials are shared upon enquiry.

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