Fungal Genome Assembly and Annotation
Hands-on workflow from raw long and short reads to a polished, annotated fungal genome ready for publication.
Programme identification
- 1.1Programme name
- Fungal Genome Assembly and Annotation
- 1.2Type of qualification
- Course
- 1.3Provider / endorsing institution
- Fungaris – International Institute of Mycology, School of Digital Mycology: AI, Genomics & Data. A Fungaris programme of its own, not endorsed by a university.
- 1.4Mode of study
- Online, with live sessions in a small group, recordings and a virtual campus.
- 1.5Duration (hours / ECTS credits)
- 3 months (12 weeks) · 72 hours in total · 6 modules of 12 hours · 12 live sessions of 2 hours. ECTS credits: not applicable (Fungaris own programme, not an official university degree).
- 1.6Language
- English
- 1.7Start and end dates / intake
- Next intake: 11 January 2027 to 2 April 2027. Enrolment closes on 4 January 2027. Following intake: 8 March 2027. How intakes work →
Overview
2.1Programme description
Fungal Genome Assembly and Annotation is a hands-on workflow course that takes you from raw sequencing reads to a polished, annotated genome ready for submission. You work on the Linux command line and a high-performance computing environment, check read quality, assemble long-read and hybrid datasets, then polish, scaffold and assess completeness with BUSCO. The second half covers gene prediction, functional annotation and the specialised annotation of repeats, biosynthetic gene clusters and effectors.
Affordable long-read sequencing means many labs can now generate fungal genomes, but poorly assembled or annotated genomes still reach public databases and mislead later studies. This course suits bioinformaticians and genomics researchers who already use the command line and want a rigorous, well-documented fungal workflow. For the final project you assemble and annotate a real fungal genome from supplied reads, report quality metrics transparently and prepare it as if for submission to a public repository.
2.2Why it matters / what need it meets
It meets a practical need: applied, up-to-date knowledge in digital mycology, useful in areas such as academic genomics, industrial biotechnology, plant health and agriculture, sequencing services.
Mycology is moving fast and good practical training is still scarce. This programme gives you a structured path, taught live by people who work in the field, so you can apply what you learn with judgement and safety.
Objectives and competences
3.1General objective
To finish the programme able to apply its content professionally and with judgement. In short:
Hands-on workflow from raw long and short reads to a polished, annotated fungal genome ready for publication.
3.2Specific objectives
- Build the foundations: Linux and HPC for genomics; Read quality control.
- Put them into practice: Long-read and hybrid assembly; Polishing, scaffolding and completeness with BUSCO.
- Apply everything to a real case: Gene prediction and functional annotation; Repeat, BGC and effector annotation.
- Complete a final project reviewed by your tutor.
3.3Competences you will gain
- Run genomics tools efficiently on Linux and HPC clusters.
- Assess sequencing read quality and estimate genome size from k-mers.
- Assemble, polish and scaffold fungal genomes from long and short reads.
- Predict and functionally annotate genes using external evidence.
- Annotate repeats, biosynthetic gene clusters and candidate effectors.
Student profile
4.1Who it is for (entry profile)
Bioinformaticians and genomics researchers.
4.2Entry requirements
Working knowledge of the Linux command line and basic genomics concepts are expected; access to a computer with internet for remote cluster use is needed.
4.3Career paths (exit profile)
- Bioinformatician in a fungal genomics laboratory
- Genome analyst at a sequencing service provider
- Computational scientist in fungal biotechnology
- Research associate in plant pathology genomics
- Bioinformatics core facility specialist
Outcomes depend on your experience and on your local market.
Study plan
5.1Overall structure (modules and workload)
| Module | Title | Phase | Topics | Hours |
|---|---|---|---|---|
| 01 | Linux and HPC for genomics | Foundations | 3 | 12 |
| 02 | Read quality control | Foundations | 3 | 12 |
| 03 | Long-read and hybrid assembly | Practice | 3 | 12 |
| 04 | Polishing, scaffolding and completeness with BUSCO | Practice | 3 | 12 |
| 05 | Gene prediction and functional annotation | Application & project | 3 | 12 |
| 06 | Repeat, BGC and effector annotation | Application & project | 3 | 12 |
| Total | 72 |
6 modules × 12 hours = 72 hours: 24 hours of live sessions, and the rest for campus study, exercises and the final project.
5.2Content by module
Hover or tap a module to follow the path from the first session to the final project. Open a module to see the topics it covers.
- Shell essentials for genomics
- Job schedulers and HPC resources
- Managing software with conda and containers
- Read formats and quality metrics
- Trimming and filtering reads
- Estimating genome size with k-mers
- Long-read assemblers compared
- Hybrid assembly strategies
- Evaluating contiguity
- Polishing with short and long reads
- Scaffolding and gap filling
- Assessing completeness with BUSCO
- Evidence-based gene prediction
- Using RNA-seq to improve models
- Functional annotation with InterPro and eggNOG
- Repeat identification and masking
- Detecting BGCs with antiSMASH
- Predicting secreted effectors
5.3Company placement
This programme does not include a company placement. Practice is built into every module through exercises, case studies and the final project.
5.4Final project
An assembled and annotated fungal genome from supplied reads, with a transparent quality and methods report.
Methodology
6.1How it is taught
- Live online sessions, usually weekly, with a working professional and a small group.
- Recordings of every session, so you can catch up if work or time zones get in the way.
- Exercises and real case studies in every module.
- Tutoring: your tutor answers questions and gives feedback on your exercises and project.
6.2Platform and resources
A Moodle virtual campus with session recordings, readings, exercises and forums for each module. You need a computer, an up-to-date browser and a stable connection; a webcam and microphone are recommended.
Technical requirements →6.3Estimated weekly workload
About 6 hours a week for 12 weeks: one 2-hour live session on a weekday evening, plus study and exercises on the campus at your own pace.
Assessment
7.1Assessment system and weighting
Progress is assessed through participation in live sessions, pipeline exercises in each module and a final project reviewed by the tutor.
7.2Requirements to pass
- Complete every module, by attending the live sessions or watching the recordings.
- Hand in the module exercises.
- Have your final project approved by your tutor.
Teaching team
8.1Academic direction
At Fungaris, the Digital Mycology school coordinates the content and quality of this programme. The academic director of each intake is named in the intake guide.
8.2Faculty
Taught by professionals who work in the field. The tutor for each intake is confirmed before the start.
Meet our faculty →Certificate
9.1Certificate awarded
Course Certificate
On completing the programme and its project, Fungaris issues a Course Certificate. Fungaris certificates are the institute's own. Whether an employer, school or authority recognises them depends on that organisation and on local rules in each country.
9.2Issuing body / recognition
Issued by Fungaris (operated by Nexora Generation, S.L.) as a digital certificate. It is a Fungaris certificate of its own: it is not an official university degree and does not award ECTS credits.
About our certificates →Admission and enrolment
10.1Admission process (steps)
- Send your request through the form or write to admissions.
- Admissions reviews your profile and confirms the start date, the session schedule and the fee.
- You secure your place with full payment or a 40% reservation.
- You receive your campus access and welcome guide before the first session.
10.2Documents required
- A valid identity document.
- Contact and billing details (personal or company).
10.3Deadlines
Enrolment for the intake starting on 11 January 2027 is open until 4 January 2027, or until the group is full (maximum 20 students).
10.4Fee and payment options
Fee: £340
- Full payment before the start: £272 (20% reduction).
- 40% reservation (£136) and 3 monthly instalments of £68.
10.5Grants, discounts and funding
Discounts: 10% for Fungaris alumni and 15% for groups of three or more people from the same organisation. Discounts cannot be combined with each other or with the full-payment reduction.
Your employer can pay for the programme and receive the invoice in the company name. Whether a public or employer training budget can cover the fee depends on your country, so check with them.
10.6Cancellation policy
The conditions for cancelling, withdrawing or moving to a later intake are explained in our cancellation policy and in your enrolment confirmation. Nothing there limits your rights under the consumer law that applies to you.
Cancellation and refunds →Additional information
11.1Frequently asked questions
Do I need experience to study Fungal Genome Assembly and Annotation?
Working knowledge of the Linux command line and basic genomics concepts are expected; access to a computer with internet for remote cluster use is needed.
How is Fungal Genome Assembly and Annotation taught?
Live online, in 6 modules with a working professional, a small group and a final project.
How am I assessed?
Progress is assessed through participation in live sessions, pipeline exercises in each module and a final project reviewed by the tutor.
What is the final project?
An assembled and annotated fungal genome from supplied reads, with a transparent quality and methods report.
What certificate do I get?
On completing the programme and its project, Fungaris issues a Course Certificate. Fungaris certificates are the institute's own. Whether an employer, school or authority recognises them depends on that organisation and on local rules in each country.
What can I study after Fungal Genome Assembly and Annotation?
The natural next step is Diploma in Fungal Bioinformatics.
11.2Alumni testimonials
We only publish verified testimonials from real students. This programme does not have any published yet; they will appear here once its first intakes finish.
11.3Admissions contact
Write to info@fungaris.institute or use the contact form. Admissions answers in your language.
Keep branching.
Join the next intake.
Pay in full with a 20% reduction, or reserve your place with 40% and pay the rest in monthly instalments. All prices are stated in pounds sterling (GBP).