GENOMICS 30 days · 6 modules · Online

Whole-Genome Assembly Workshop (30-Day, Online)

Estimate genome size, assemble, polish and annotate genomes from short and long sequencing reads.

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About this workshop

Assembling a genome means reconstructing a full sequence from millions of short or long fragments, with no reference to guide you. Quality depends on decisions made before assembly starts, such as how large and repetitive the genome is and which reads to use. This workshop begins with estimating genome size and complexity from the reads, then compares short-read, long-read and combined strategies. You learn how to polish an assembly, judge it with statistics and completeness checks, and remove contamination and duplicated sequence. The second half covers annotation: masking repeats, predicting genes and assigning functions to them. By the end you will have taken a small genome from raw reads to an annotated assembly and will know how to judge the quality of other people's.

Tools and pipelines you will use

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

FastQC ↗Flye ↗Hifiasm ↗SPAdes ↗Medaka ↗Racon ↗BUSCO ↗QUAST ↗RepeatMasker ↗BRAKER ↗

What you will learn

Module 1 Foundations
Week 1
Linux and command-line basics Run tools and plan storage.
Genome assembly concepts Reads, contigs, scaffolds and chromosomes.
Sequencing technologies Short reads, long reads and when to combine them.
Read quality control Evaluate and clean reads.
Module 2 Genome characteristics
Genome size estimation Estimate size and complexity from k-mers.
Heterozygosity and repeats Know what to expect before assembly.
Resource planning Estimate memory and time needs.
Read preparation Select and correct reads for assembly.
Module 3 Assembly
Short-read assembly Build contigs from short reads.
Long-read assembly Build longer, more contiguous sequences.
Hybrid approaches Combine read types.
Comparing assemblies Test different tools and settings.
Module 4 Polishing and quality
Error correction Polish the assembly with reads.
Assembly statistics Interpret N50 and other metrics.
Completeness checks Test for expected core genes.
Contamination and duplicates Find and remove unwanted sequence.
Module 5 Annotation
Repeat identification Find and mask repeats.
Gene prediction Predict genes with evidence and models.
Functional annotation Assign names, domains and GO terms.
Annotation summary Report gene counts and features.
Module 6 Mini-project and report
Week 4
Project dataset Assemble and annotate a small genome.
Reproducible workflow Record every step and setting.
Figures and write-up Present assembly and annotation results.
Review and next steps Discuss scaffolding and improvement.

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 Whole-Genome de novo Assembly 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 k-mer genome profiling, long-read assembly with Flye and Hifiasm, hybrid polishing with short reads, assembly evaluation using QUAST and BUSCO, repeat masking, and gene prediction using BRAKER.

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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