Computational Genomics workshops

Build a statistically rigorous RNA-seq analysis in R and Bioconductor. The workshop develops data import and visualisation skills, hypothesis testing and genomic interval analysis before covering read mapping, count normalisation, differential expression and multiple-testing correction. Practical comparisons include DESeq2, edgeR and limma/voom. The final session interprets functional pathways using overrepresentation and permutation-based gene-set enrichment analysis. Six live online sessions on 2, 3, 5, 6, 9 and 10 November, 15:00–18:00 Europe/Berlin (CET). Fee €530. Basic R programming and genomics knowledge are expected; previous statistical training is unnecessary.

This practical school introduces bulk RNA-seq analysis for biologists and data analysts with little computing experience. Participants work through Linux commands, sequencing technologies and file formats, quality assessment and trimming, read alignment, mapping diagnostics and visualization using an Illumina dataset. Later sessions compare methods for quantifying transcripts and detecting differential gene expression, splicing and isoform expression, with R graphics and exercises to interpret the results. Single-cell RNA-seq analysis is outside the programme. Teaching runs from 09:00 to 17:00 on 2–5 November 2026, local Berlin time (CET, UTC+1). A basic understanding of molecular biology is expected. Instruction is in English; workstations and course materials are supplied. The fee is EUR 1,449 excluding VAT, with travel and accommodation additional. The course has a 30-person capacity, allocated in order of registration and subject to seat confirmation; the form may place applicants on a waiting list. Registration closes on 30 October.

Transposable-element biology and evolution are connected with practical bioinformatic methods for identifying and analysing repetitive DNA. Participants examine how these mobile sequences influence genome structure, gene regulation and epigenetic states, and why their rapid evolution complicates computational annotation. The programme combines conceptual instruction with analysis exercises across the published five-day schedule. Teaching runs online from 14:00 to 19:00 Berlin time. The listed course package costs €480.

This hands-on workshop introduces metagenomic analysis with MOTHUR on Galaxy Australia. Participants will explore how sequencing data reveal microbial community composition, diversity and functional potential. Practical work follows raw-read quality control, OTU clustering, taxonomic classification and diversity analysis in Galaxy’s browser interface, including filtering, profiling and visualisation. The training combines core concepts with workflows participants can use for their own microbial ecology and environmental genomics projects. The online workshop runs 10:00–18:00 AEDT (Australia/Sydney, UTC+11) on 4 November 2026, equivalent to 09:00–17:00 AEST, 09:30–17:30 ACDT or 07:00–15:00 AWST. It is free, with essential applications and limited places, and is open to Australian researchers and students in the life sciences. Familiarity with Galaxy, or completion of an introductory Galaxy workshop, is recommended; coding experience is not required. A Galaxy Australia account is needed. UQ staff and students use the UQ application route; other Australian researchers use Eventbrite.

This practical course introduces next-generation sequencing and the core bioinformatics analyses used with sequencing data. Participants work through quality control and read mapping, learning standard file formats, quality-score encoding and common analysis tools. It is designed for life scientists and computer scientists preparing to analyse NGS data. Familiarity with Galaxy or prior introductory Galaxy training is recommended, and participants need a Galaxy Australia account, their own computer and a reliable internet connection. The online course runs on 4 and 5 November, 13:00–17:00 AEST each day (14:00–18:00 AEDT); participants must attend both sessions. The training is free for Australian researchers under the collaboration between QCIF, Australian BioCommons and the National Bioinformatics Training Cooperative. Applications are required, and Zoom setup details are provided to participants before the course.

Assemble eukaryotic genomes by combining long-read sequencing with chromatin-contact data. Practical work progresses from read manipulation and k-mer analysis through assembly algorithms, removal of duplicated haplotigs and Hi-C scaffolding. Participants assess contiguity, sequence accuracy and gene completeness with approaches including Merqury and BUSCO, and finish by comparing results from small eukaryotic datasets. The theoretical component explains how repeats, heterozygosity and sequencing technologies influence assembly choices. Sessions: 9–13 November, 14:00–20:00 daily, Europe/Berlin (CET, UTC+01:00). Live online training; fee €530. Suitable for researchers learning de novo assembly, including beginners; Linux practice is included. An optional €900 bundle includes the separate manual-curation course.

Use Hi-C contact maps to diagnose and correct assembly errors and produce chromosome-scale genome sequences. The workflow starts with assembly metrics and contamination screening, then constructs PretextView maps and supporting tracks and applies a rapid-curation pipeline to generate corrected FASTA files. Exercises address repeats, haplotype duplication and phasing, microchromosomes, polyploid genomes and sex-chromosome identification. Group work culminates in evaluating and discussing difficult assemblies. Sessions: 16–20 November, 14:00–18:00 daily, Europe/Berlin (CET, UTC+01:00). Live online training; fee €480. Biological background is expected. Unix command-line skills are mandatory for running scripts; previous assembly experience is helpful. An optional €900 bundle includes the separate genome-assembly course.

A five-day practical course for experimentalists and computational biologists analysing single-cell RNA sequencing. Lectures and exercises follow data from sequencing files to expression matrices, quality control, normalisation, batch correction, dimensionality reduction, clustering, annotation and differential expression. Later sessions cover trajectory and pseudotime inference, RNA velocity, single-cell multi-omics integration and functional analysis. Participants finish with an independent dataset analysis and presentation. Bash and R/Bioconductor support reproducible workflows and interpretation. Online, 16–20 November 2026, 14:00–20:00 CET (Europe/Berlin) each day. Fee: €530. Participants need practical Unix command-line skills, R programming experience and familiarity with next-generation sequencing analysis.

Build a small-RNA analysis workflow from raw reads to curated microRNA annotations. Participants assess sequencing quality with miRTrace, retrieve public datasets and reproduce analyses and figures from published studies. Practical work combines MirMachine, miRTrace and MirMiner with genomic context and annotation standards, then examines false positives and missing genes through manual curation. The emphasis is on defensible identification of regulatory microRNAs and critical assessment of published predictions. Sessions: 23–26 November, 12:00–17:00 daily, Europe/Berlin (CET, UTC+01:00). Live online training; fee €480. Basic small-RNA biology and genomics, Unix/Linux shell and conda familiarity are expected.

Analyse microbial communities from shotgun sequencing using reproducible computational workflows. The workshop covers read preprocessing, taxonomic and strain-level profiling, functional characterisation, metagenome assembly and reconstruction of microbial genomes. Exercises use tools including MetaPhlAn, StrainPhlAn, PanPhlAn, HUMAnN, MEGAHIT and PhyloPhlAn, while comparing short- and long-read approaches. Statistical sessions address community diversity, high-dimensional testing, regression and classification, followed by visualisation and reusable scientific reports. Live online, 23–26 November, 14:00–20:00 Europe/Berlin (CET). Fee €530. Basic command-line knowledge is helpful; preparatory Unix material is provided.

This live course introduces sequencing-data analysis through a real Illumina dataset. It explains how sequencing technologies affect data quality and interpretation, then develops the Linux and file-format skills needed for practical analysis. Exercises cover quality control, adapter removal, read mapping, alignment statistics, genome-browser visualization, DNA variant calling, VCF filtering and interpretation. Participants compare analytical tools and learn to recognize errors that can affect biological conclusions. The online sessions run 09:00–17:00 CET (UTC+1) on 23–25 November 2026. The course is taught in English for biologists and data analysts with basic molecular-biology knowledge; prior Linux experience is unnecessary. A computer, current browser and audio equipment are required. Exercises use a supplied cloud computer through the browser. The fee is EUR 879 excluding VAT and includes printed materials and cloud access. Capacity is 25, with places subject to confirmation and a waiting list if full. Registration closes on 22 November. Sessions are live and build sequentially, so continuous attendance is expected.

Create interactive, reproducible views of omics datasets with the iSEE Bioconductor framework. Participants configure linked panels, inspect bulk and single-cell RNA data and preserve exploratory workflows. Guided cookbook exercises progress to independent exploration, collections of datasets and participants’ own projects, with troubleshooting and companion-package demonstrations. The framework also supports spatial and proteomic data represented by SummarizedExperiment objects. Sessions: 25–26 November, 13:00–17:00 daily, Europe/Berlin (CET, UTC+01:00). Live online training; fee €280. For advanced MSc, doctoral and postdoctoral researchers. Familiarity with sequencing data, common single-cell data containers and visualisation is helpful.

Detect and interpret genomic alterations of at least 50 bases using short and long reads. Lectures and practical exercises compare assembly-based and reference-mapping workflows, evaluate sequencing and assembly quality, and filter and annotate structural variants. Participants build trio or population VCF datasets, examine mosaic and somatic variation, and prioritise possible functional effects using human-genome examples. Linux and cloud exercises connect raw data processing with interpretation of disease and phenotype associations. Sessions: 30 November–2 December, 14:00–20:00 daily, Europe/Berlin (CET, UTC+01:00). Live online training; fee €450. A biology background and familiarity with genomic data formats are expected. Command-line Linux practical work is introduced during the course.

Infer evolutionary relationships and divergence times from multilocus genomic data while accounting for sources of misleading phylogenetic signal. The workshop examines orthologue selection, sequence-evolution models and discordance caused by incomplete lineage sorting and introgression. Lectures and hands-on exercises develop time-calibrated phylogenies and compare the assumptions of alternative inference methods. Analyses run in a prepared cloud environment so participants can concentrate on statistical methods, model choices and interpretation. Live online, 30 November–4 December, 12:00–18:00 Europe/Berlin (CET). Fee €530. Intended for PhD and postdoctoral researchers planning multilocus phylogenetic studies. Basic Unix command-line knowledge is required; familiarity with scripting is useful.

This workshop connects genomic discovery with prediction of epilepsy outcomes. It examines genome-based multi-omics in multigenerational cohorts, multimodal deep learning that combines clinical and genomic information to predict antiseizure medication response, and polygenic risk scores integrated with machine learning to estimate disease severity and seizure control. The presentations link these complementary approaches to the problem of clinical heterogeneity and assess their practical role in more individualized treatment. Sunday 6 December, 14:00–15:30 Mountain Standard Time (America/Denver). Part of the 2026 American Epilepsy Society Annual Meeting. In-person meeting registration and a free myAES account are required. Standard full-meeting rates are USD 800 for member scientists and USD 1,075 for non-member scientists; student rates are USD 250 and USD 360, respectively. Other professional and one-day categories are available. Seating priority goes to registered attendees.

Learn how reduced-representation sequencing produces markers for population genetics, phylogenetics and association studies in non-model organisms. The workshop follows Stacks workflows from short-read quality assessment and preprocessing through de novo or reference-based locus assembly to informative variant selection. Lectures and guided exercises examine how study design changes the analysis, with time to interpret results and work on participants' datasets. Live online, 7–11 December, 14:00–19:00 Europe/Berlin (CET). Fee €530. Intended for researchers and technical staff with a biology background and familiarity with high-throughput genomic data; Unix concepts are introduced.

Analyse native RNA molecules with nanopore sequencing, concentrating on RNA004 chemistry and its distinctive computational challenges. The course follows POD5 inspection and quality assessment through basecalling, alignment, transcript discovery and abundance estimation. Later exercises estimate poly(A) tails and detect RNA modifications; small projects examine mRNA isoforms, m6A or tRNA modifications, or participants’ own data. Discussions place these analyses in the context of technological limits and emerging applications. Sessions: 14–17 December, 15:00–19:00 daily, Europe/Berlin (CET, UTC+01:00). Live online training; fee €480. Familiarity with RNA sequencing and strong Unix/Linux or macOS shell experience are required.

Analyze gene expression within tissue using imaging-based and sequencing-based spatial transcriptomics. Guided R/Bioconductor labs cover cell segmentation, quality control, interactive exploration and integration with single-cell datasets. Downstream analyses characterize cellular niches, neighbourhoods and cell–cell communication. The course concludes with project design and a team hackathon using participant or public data, connecting computational outputs to biological interpretation. 2026-12-14–2026-12-18, 14:00–18:00 daily, Europe/Berlin (CET, UTC+01:00). Online course; fee €530. Designed for advanced students and researchers with basic R and Bioconductor proficiency.

Create and interpret visualisations for expression, genomic and comparative-genomic studies in R. The workshop starts with volcano plots, dimensionality-reduction displays, genomic peaks, pathways and heatmaps. It then covers genome coverage, alignments, Manhattan plots and temporal allele-frequency changes, followed by phylogenetic trees, set intersections, circos displays, synteny, ideograms and pangenome graphs. Practical work connects each display to the biological structure of the data. Live online, 14–16 December, 13:00–18:00 Europe/Berlin (CET). Fee €420. Familiarity with R is expected; a short introductory R resource is provided.

Comparative genomics and single-cell transcriptomics are combined to investigate cell-type evolution. Guided exercises progress from orthology inference and gene-family trees to single-cell preprocessing, clustering and annotation, followed by cross-species comparisons. The course examines duplication, gene loss, study design and how evolutionary relationships among genes affect proposed correspondences between cell populations. It also addresses limitations of using expression similarity as evidence for cell-type homology. The audience is postgraduate students and researchers with basic evolutionary and genomics knowledge. Sessions run 14:00–18:00 Berlin time; the listed course fee is €480.