School of Bioinformatics · Genomics & transcriptomics
Long-Read Sequencing: Nanopore & PacBio Analysis
Long reads resolve repeats, structural variants and full-length transcripts that short reads cannot. This course covers the complete long-read toolkit, from raw signal to biological result, for both Oxford Nanopore and PacBio HiFi data.
Course overview
Long-Read Sequencing teaches the analyses that make long reads worth their cost: phased variant calling, structural-variant discovery, isoform-level transcriptomics and the detection of DNA modifications directly from the sequencing signal.
Each module compares platforms honestly, covering error profiles, coverage needs and which questions each technology answers best, so that you can plan a long-read experiment as well as analyse one.
Learning outcomes
By the end of the course you will be able to:
- Explain how Nanopore and PacBio HiFi reads are generated and where their errors come from
- Basecall, demultiplex and quality-check long-read data
- Align long reads and call small and structural variants with phasing
- Identify full-length transcript isoforms
- Detect 5mC methylation from Nanopore data
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
- NGS Data Analysis or equivalent experience
- Comfortable on the Linux command line
Best suited to
- Genomics researchers adopting Nanopore or PacBio
- Bioinformaticians working on structural variation or isoforms
- Core-facility staff supporting long-read users
Module-wise syllabus
6 modules. Each pairs instructor-led sessions with a hands-on lab on public data.
Topics
- Nanopore signal and PacBio HiFi
- Error profiles and accuracy
- Experimental design and coverage
Topics
- Basecalling models with Dorado
- Demultiplexing and adapter trimming
- Read-level QC
Topics
- minimap2 presets
- Variant calling with Clair3 and DeepVariant
- Phasing with WhatsHap
Topics
- SV types and signatures
- Sniffles2 and cuteSV
- Benchmarking and visualisation
Topics
- Full-length cDNA and direct RNA
- Isoform discovery
- 5mC calling with modkit
Topics
- Study design
- Analysis
- Platform recommendation
Practical sessions and projects
Capstone project
Answer a question only long reads can
Analyse a public long-read dataset to resolve structural variants or isoforms that short reads miss, and recommend a design for a follow-up experiment.
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.
- Long-read technologies
Compare the length and quality distributions of Nanopore and HiFi runs of the same sample with NanoPlot.
- From signal to reads
Basecall a small Nanopore dataset with two accuracy models and measure the difference against a reference.
- Alignment and small variants
Call and phase SNVs and indels in a human benchmark region and score them against the GIAB truth set.
- Structural variants
Discover deletions, insertions and inversions and inspect them in IGV.
- Transcripts and modifications
Identify novel isoforms in a long-read transcriptome and summarise CpG methylation over promoters.
- Project: a long-read study
Analyse a public long-read dataset end to end and recommend the platform and depth for a follow-up study.
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
- Genome in a Bottle HG002 long reads: Benchmarking variant calls.NIST GIAB (public)
- Public Nanopore cDNA runs: Isoform analysis.ENA / SRA
Core reading
- Li H (2018). Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34:3094–3100.
- Logsdon GA, Vollger MR, Eichler EE (2020). Long-read human genome sequencing and its applications. Nature Reviews Genetics 21:597–614.
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 Long-Read Sequencing: Nanopore & PacBio Analysis, 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 Long-Read Sequencing: Nanopore & PacBio Analysis
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. Heavy labs run on the course server. 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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