School of Bioinformatics · Genomics & transcriptomics
Genome Assembly & Annotation
Sequencing a new organism, strain or isolate means building its genome from millions of fragments. This course covers how assemblers work, how to choose and run one for your data, and how to judge and annotate the result.
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Course overview
Genome Assembly & Annotation explains the graph ideas behind modern assemblers (de Bruijn graphs for short reads, overlap and repeat graphs for long reads) so that you can read an assembly report critically rather than trusting the longest N50.
You assemble bacterial and small eukaryotic genomes from Illumina, Oxford Nanopore and hybrid data, polish them, measure their completeness and correctness, and annotate genes and functions. The capstone is a complete, submission-ready genome.
Learning outcomes
By the end of the course you will be able to:
- Explain de Bruijn and overlap-graph assembly and their failure modes
- Assemble genomes from short, long and hybrid read sets
- Polish assemblies and evaluate them with QUAST, BUSCO and read mapping
- Annotate prokaryotic and eukaryotic genomes structurally and functionally
- Prepare an assembly and annotation for submission to a public archive
Skills you will practise
Eligibility and prerequisites
Who can apply
- Students and graduates of B.Sc., M.Sc., B.Tech., M.Tech., B.Pharm., M.Pharm., MBBS, BDS, B.V.Sc. or a PhD programme in the life sciences, biotechnology, bioinformatics, pharmacy, medicine, agriculture, chemistry, statistics or computer science
- Researchers, faculty and industry professionals moving into data-driven biology
- Final-year students may apply before their results are declared
Prerequisites
- Linux command line
- Bioinformatics Foundations or equivalent
Best suited to
- Microbiologists and biotechnologists sequencing new isolates
- Students working on non-model organisms
- Bioinformaticians adding assembly to their toolkit
Module-wise syllabus
6 modules. Each pairs instructor-led sessions with a hands-on lab on public data.
Topics
- k-mers and de Bruijn graphs
- Overlap graphs and repeats
- Coverage, errors and ploidy
Topics
- SPAdes and its modes
- Choosing k and coverage
- Contamination checks
Topics
- Nanopore and PacBio read characteristics
- Flye assembly and circularisation
- Hybrid strategies and polishing
Topics
- Contiguity versus correctness
- QUAST, BUSCO and read-back mapping
- Misassemblies and how to find them
Topics
- Prokka and Bakta for prokaryotes
- Evidence-based eukaryotic annotation with BRAKER
- Functional annotation and orthology
Topics
- Assembly report
- Annotation files
- Archive submission requirements
Practical sessions and projects
Capstone project
Assemble and annotate a genome
Produce a polished, annotated genome from raw short and long reads, justify every choice with QC evidence, and prepare the files for archive submission.
Assessed on the correctness of the analysis, the quality of the code and the reasoning in the write-up. A pass is required for the certificate.
- How assemblers work
Estimate genome size and heterozygosity from k-mer spectra and predict which regions will be hard to assemble.
- Short-read assembly
Assemble a bacterial genome from Illumina reads with SPAdes and screen the contigs for contamination.
- Long-read and hybrid assembly
Assemble the same isolate from Nanopore reads with Flye, polish it with short reads and compare the two assemblies.
- Assessing an assembly
Benchmark three assemblies of one genome and decide which you would submit, with evidence.
- Annotation
Annotate the bacterial assembly, assign functions and find its resistance and virulence genes.
- Project: a submission-ready genome
Deliver an assembled, polished and annotated genome with a quality report that meets public-archive submission standards.
Software, tools and datasets
Software and tools
All software is free and open source or free for academic use. Recommended computer: 8 GB RAM, 30 GB free disk, Linux, macOS or Windows with WSL2.
Datasets
- Bacterial isolate with Illumina and Nanopore reads: Short, long and hybrid assembly.NCBI SRA (public)
- Saccharomyces cerevisiae reference reads: Eukaryotic assembly and annotation.NCBI SRA
Core reading
- Kolmogorov M, Yuan J, Lin Y, Pevzner PA (2019). Assembly of long, error-prone reads using repeat graphs. Nature Biotechnology 37:540–546.
- Bankevich A et al. (2012). SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology 19:455–477.
- Simão FA et al. (2015). BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31:3210–3212.
Duration, format and fees
- Next cohort
- Dates are sent with your admission offer
- Timetable
- Three evening or weekend sessions a week (IST), plus a lab clinic; intensive and weekend-only schedules on request
- Payment
- Secure online payment link with your admission offer (UPI, cards, net banking). Instalments on request for fees above ₹15,000.
- Refunds
- See the refund and cancellation policy.
Instructor
The instructor for each cohort is named in your admission offer and on this page when the cohort is announced. Vedicgen instructors are selected for hands-on research or industry experience in the subject they teach, and every course is reviewed by a second subject expert.
Questions about who teaches a cohort? [email protected]
Certificate
Learners who complete the course and pass its capstone receive a Vedicgen certificate of completion for Genome Assembly & Annotation, issued by Vivofold, stating the guided hours and skills assessed. Each certificate has a unique ID and QR code that anyone can check.
Apply for Genome Assembly & Annotation
Apply
Send the form below. It takes about five minutes.
Review
An adviser confirms your fit and format within two working days.
Offer
You receive dates, timetable and a secure payment link.
Onboard
Set-up guide, pre-reading and joining links.
Frequently asked questions
In the live cohort, modules are taught in instructor-led sessions with a weekly lab clinic where you work on real public data with help at hand; every session is recorded. The self-paced format uses the same lessons, labs and datasets with mentor review of your capstone. Both formats end with an assessed project reviewed for the code and the science.
A laptop with at least 8 GB of RAM and about 30 GB of free disk space, running Linux, macOS, or Windows with WSL2. Assembly labs run on the course server, so a modest laptop is enough. Installation instructions are sent before the first session, and lab clinics help with any set-up problems.
Yes. Learners who complete the course and pass its assessment receive a Vedicgen certificate of completion, issued by Vivofold. Every certificate carries a unique ID and a QR code that anyone, including an employer or admissions office, can check on the certificate verification page.
Apply with the form on this page. Live and in-person cohorts run through the year; the dates, timetable and joining details of the next cohort are sent with your admission offer and listed on this page once announced. Self-paced enrolment opens as soon as your application is accepted.
Yes. No course runs longer than four weeks, and the length is customisable: choose the standard schedule, an intensive one- to two-week schedule, weekends only, or a custom timetable. Pick your preference on the application form; colleges and teams can book their own dates.
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