Events‌ and Workshops

Due to the rapid decrease in the cost of sequencing, sample preparation is often the bottleneck in next-generation sequencing (NGS) workflows. Volume miniaturization with automated liquid handlers has the potential to solve throughput and cost challenges, enabling researchers to process more samples while generating more data.

In this webinar, Richard Eccles from the Centre for Genomic Research at the University of Liverpool alongside SPT Labtech, and New England Biolabs, Inc. demonstrate how the mosquito^® genomics enables the automation and miniaturization of the NEBNext^® Ultra^™ II FS DNA library prep kit, producing high quality data, increased throughput, and a significant reduction in the cost per sample.

Join this webinar to find out:

• How to automate library prep at 1/10th of original volumes, while maintaining sequence coverage and quality comparable with full-volume reactions
• The possibility of miniaturization and automation of solid-phase reversible immobilization (SPRI) bead purification
• An overview of mosquito® genomics, dragonfly^® discovery instruments and related accessories from SPT Labtech
• How to generate high-quality sequencing data from a wide range of input amounts and sample types

The event is an excellent opportunity for learning more about the platforms available at the CGR for your research. Our co-director Prof Steve Paterson will provide an overview of the CGR services and collaborations. He will launch a competition for sequencing a de novo genome in partnership with the Nerc Environmental Omics facility (NEOF) and the Wellcome Trust Sanger Institute’s Darwin Tree of Life (DToL) project.

We have two great speakers who will deliver a talk on how they used long reads to accelerate their research. Dr Chris Quince will provide an overview of his latest research in the Microbiome. At the same time, our co-director Prof Alistair Darby will give an insight into Arthropod Genomics for Pest and Disease Control.

Finally, the Q&A section will allow you to interact with:

Kirren Kaur (PacBio Field Applications Specialist)

Bas Tolhuis (PacBio Field Applications Scientist, Bioinformatics) from PacBio

Dr Anita Lucaci (CGR Sequence Production Manager) 

Dr Xuan Liu (CGR Informatics Team) 

They will join the panel to answer any questions you may have on applications or collaborating with CGR. 

The event is a unique opportunity for finding more on how to use long reads and collaborate with the Centre for Genomics.

Centre for Genomic Research and Computational Biology Facility, University of Liverpool 

The workshop will take place over 5 days. Each day will consist of 2 half-day sessions, each consisting of a ~1 hour lecture followed by 2 hours of practical exercises. Python is a dynamic, readable language that is a popular platform for all types of bioinformatics work, from simple one-off scripts to large, complex software projects. This workshop is aimed at complete beginners and assumes no prior programming experience. It gives an overview of the language with an emphasis on practical problem-solving, using examples and exercises drawn from various aspects of bioinformatics work. The workshop is structured so that the parts of the language most useful for bioinformatics are introduced as early as possible, and that students can start writing plausibly-useful programs after the first few sessions. After completing the workshop, students should be in a position to (1) apply the skills they have learned to tackling problems in their own research and (2) continue their Python education in a self-directed way.

The instructor of the workshop is the Founder of Python for Biologists, Dr. Martin Jones. 

Centre for Genomic Research and Computational Biology Facility, University of Liverpool 

Centre for Genomic Research and Computational Biology Facility, University of Liverpool 

Centre for Genomic Research and Computational Biology Facility, University of Liverpool 

Centre for Genomic Research, University of Liverpool

16S rRNA gene profiling (metagenetics) and shotgun sequence based metagenomics are now well established and can be utilised to characterise complex populations. The course will provide a 3-day introduction to the conceptual and practical issues involved in analysing such datasets, generated from the Illumina NGS platforms, and comprises the following sessions:

• Sequence data QC and preparation for downstream analyses
• Metagenomic shotgun sequence analysis.
• Taxonomic profiling (MetaPhlAn)
• Metagenome assembly (MEGAHIT) and annotation (Prokka)
• Functional annotation (Cognizer)
• Data visualisation
• Analysis of 16S rRNA data with QIIME
• Laboratory tour of sequencing laboratory
• Metagenome functional prediction using metagenetic data

Feedbacks from partecipants:

"It was great learning from trainers who are experts in the field"

"The course was well structured with the information given in the the talks relevant to the next practical session. It was useful to learn the theory behind each step in the analysis and the have the opportunity to perform the analysis in the practicals".

Centre for Genomic Research, University of Liverpool

The course is presented by the Centre for Genomic Research and the Computational Biology Facillity at the University of Liverpool. We offer keynote talks by experts in the areas covered and a large portion of the course comprises practical computer sessions, allowing delegates to obtain hands-on experience.

This course is designed to provide a 2.5-day introduction to the conceptual, practical and interpretational issues involved in large-scale gene expression profiling. Whole transcriptome profiling is now well established, and can be applied to a wide range of biological questions. However, it is challenging both in handling the huge amounts of data generated, and downstream interpretation.

This course covers aspects associated with next-generation sequencing-based approaches to transcriptional profiling (RNA-Seq), comprising the following sections:

• Introduction to next-generation sequencing, sequencing QC and RNA-Seq
• Experimental design and cost implications
• Laboratory tour of sequencing laboratory
• Mapping and visualising RNAseq data
• Multi-omics data integration

Centre for Genomic Research, University of Liverpool

This 3-day bioinformatics course is presented by the Centre for Genomic Research and funded by the Natural Environment Research Council (NERC). It primarily focuses on practical computer sessions designed to provide delegates with hands-on experience of the informatics involved in analysing metagenomic and metagenetic datasets.

16S rRNA gene profiling (metagenetics) and shotgun sequence based metagenomics are now well established and can be utilised to characterise complex populations. The course will provide a 3-day introduction to the conceptual and practical issues involved in analysing such datasets, generated from the Illumina NGS platforms, and comprises the following sessions:

• Sequence data QC and preparation for downstream analyses
• Metagenomic shotgun sequence analysis.
• Taxonomic profiling (MetaPhlAn)
• Metagenome assembly (MEGAHIT) and annotation (Prokka)
• Functional annotation (Cognizer)
• Data visualisation
• Analysis of 16S rRNA data with QIIME
• Laboratory tour of sequencing laboratory
• Metagenome functional prediction using metagenetic data

Centre for Genomic Research, University of Liverpool

This bioinformatics course is presented by the Centre for Genomic Research and funded by the Natural Environment Research Council (NERC). It primarily focuses on practical computer sessions designed to provide delegates with hands-on experience of the informatics involved in analysing metagenomic and metagenetic datasets.

The 16S rRNA gene profiling (metagenetics) and shotgun sequence based metagenomics are now well established and can be utilised to characterise complex populations. The course will provide a 2-day introduction to the conceptual and practical issues involved in analysing such datasets, generated from the Illumina NGS platforms, and comprises the following sessions:

• Introduction to Unix and the command line.
• Sequence data QC and preparation for downstream analyses
• Metagenomic shotgun sequence analysis.
• Taxonomic profiling (MetaPhlAn)
• Metagenome assembly (MEGAHIT) and annotation (Prokka)
• Functional annotation (Cognizer)
• Data visualisation
• Analysis of 16S rRNA data with QIIME

Centre for Genomic Research, University of Liverpool 

The course is presented by the Centre for Genomic Research and the Centre for Computational Biology and Modeling at the University of Liverpool. We offer keynote talks by experts in the areas covered and a large portion of the course comprises practical computer sessions, allowing delegates to obtain hands-on experience.

This course is designed to provide a 4-day introduction to the conceptual, practical and interpretational issues involved in large-scale gene expression profiling. Whole transcriptome profiling in now well established, and can be applied to a wide range of biological questions. However, it is challenging both in handling the huge amounts of data generated, and downstream interpretation.

This course covers aspects associated with next-generation sequencing-based approaches to transcriptional profiling (RNA-Seq), comprising the following sections:

• Introduction to next-generation sequencing and RNA-Seq
• Experimental design and cost implications
• Laboratory tour of sequencing laboratory
• Informatic issues: The command-line interface, Data handling and statistical analyses, Analysis in the iPlant environment, Network modelling

Centre for Genomic Research, University of Liverpool 

This bioinformatics course is presented by the Centre for Genomic Research and funded by the Natural Environment Research Council (NERC). It primarily focuses on practical computer sessions designed to provide delegates with hands-on experience of the informatics involved in analysing metagenomic and metagenetic datasets.

The 16S rRNA gene profiling (metagenetics) and shotgun sequence based metagenomics are now well established and can be utilised to characterise complex populations. The course will provide a 2-day introduction to the conceptual and practical issues involved in analysing such datasets, generated from the Illumina NGS platforms, and comprises the following sessions:

• Introduction to Unix and the command line.
• Sequence data QC and preparation for downstream analyses
• Metagenomic shotgun sequence analysis.
• Taxonomic profiling (MetaPhlAn)
• Metagenome assembly (MEGAHIT) and annotation (Prokka)
• Functional annotation (Cognizer)
• Data visualisation
• Analysis of 16S rRNA data with QIIME

University of Malawi, College of Medicine

(Sponsored by the BBSRC IAA award to FHLS)

ILRI Kenia

(Sponsored by the BBSRC IAA award to FHLS)

Working with Parasite Database Resources (Wellcome Trust Advanced Courses program) 16th – 21st October 2016

Institute of Hygiene, Montevideo, Uruguay

Centre for Genomic Research, University of Liverpool  

The course is presented by the Centre for Genomic Research at the University of Liverpool and sponsored by the Physiological Society. We offer keynote talks by experts in the areas covered and a large portion of the course comprises practical computer sessions, allowing delegates to obtain hands-on experience.

This course is designed to provide a 4-day introduction to the conceptual, practical and interpretational issues involved in large-scale gene expression profiling. 

This course covers aspects associated with next-generation sequencing-based approaches to transcriptional profiling (RNA-Seq), comprising the following sections:

• Designing a RNAseq gene expression experiment
• Quality control and library preparation
• Introduction to CyVerse: Data preparation and analysis
• Laboratory tour of sequencing laboratory
• Informatic issues: The command-line interface, Data handling and statistical analyses, Analysis in the iPlant environment, Network modelling

Hinxton, Cambridgeshire

Centre for Genomic Research, University of Liverpool

This bioinformatics course is presented by the Centre for Genomic Research and funded by the Natural Environment Research Council (NERC). It primarily focuses on practical computer sessions designed to provide delegates with hands-on experience of the informatics involved in analysing metagenomic and metagenetic datasets.

The course will provide a 2-day introduction to the conceptual and practical issues involved in analysing such datasets, generated from the Illumina NGS platforms, and comprises the following sessions:

• Introduction to shotgun metagenomic sequence analysis
• Sequence data QC and preparation for downstream analyses
• Analysis of 16S rRNA data with QIIME

Centre for Genomic Research, University of Liverpool 

The course is presented by the Centre for Genomic Research at the University of Liverpool and funded by the Physiological Society and Natural Environment Research Council (NERC). We offer keynote talks by experts in the areas covered and a large portion of the course comprises practical computer sessions, allowing delegates to obtain hands-on experience.

This course is designed to provide a 4-day introduction to the conceptual, practical and interpretational issues involved in large-scale gene expression profiling. 

This course covers aspects associated with next-generation sequencing-based approaches to transcriptional profiling (RNA-Seq), comprising the following sections:

• Introduction to next generation sequencing and RNAseq
• Designing a gene expression experiment, microarray and RNAseq
• Transcriptome and genome assembly and gene annotation
• Quality control and library preparation 
• Reverse engineering biological pathways from observational data
• Informatic issues: The command-line interface, Data handling and statistical analyses, Network modelling

GARNet and Centre for Genomic Research at the University of Liverpool

Software Carpentry teaches principles of good programming applicable to any coding language or application, whether sequencing data, phenotypic trait analysis or biochemical assays. Tutorials will start from first principles and cover Python programming, managing data in Excel and Python; and scientific plotting using BioPython and R. Teaching will be a combination of live coding guided by the trainer and independent practical exercises.

Introducing biologists to:

• Git and GitHub
• Python programming
• Version control
• Good practice and test-driven development 
• Applying data managment aand scientific programming to your project.

Centre for Genomic Research, University of Liverpool 

The course is presented by the Centre for Genomic Research at the University of Liverpool and funded by the Physiological Society. We offer keynote talks by experts in the areas covered and a large portion of the course comprises practical computer sessions, allowing delegates to obtain hands-on experience.

This course is designed to provide a 5-day introduction to the conceptual, practical and interpretational issues involved in large-scale gene expression profiling. 

This course covers aspects associated with next-generation sequencing-based approaches to transcriptional profiling (RNA-Seq), comprising the following sections:

• Introduction to next generation sequencing and RNAseq
• Designing a gene expression experiment, microarray and RNAseq
• Transcriptome and genome assembly and gene annotation
• Quality control and library preparation 
• Mapping and visualizing RNAseq data
• Reverse engineering biological pathways from observational data
• Informatic issues: The command-line interface, Data handling and statistical analyses, Network modelling

Centre for Genomic Research, University of Liverpool 

The course is presented by the Centre for Genomic Research at the University of Liverpool and funded by the Physiological Society and in collaboration with the University of Sheffield. We offer keynote talks by experts in the areas covered and a large portion of the course comprises practical computer sessions, allowing delegates to obtain hands-on experience.

This course is designed to provide a 4-day introduction to the conceptual, practical and interpretational issues involved in large-scale gene expression profiling. 

This course covers aspects associated with next-generation sequencing-based approaches to transcriptional profiling (RNA-Seq), comprising the following sections:

• Advantages of nextgeneration sequencing over microarrays – gene discovery, transcriptome discovery
• Quality control and library preparation 
• Designing a gene expression experiment, microarray and RNAseq
• The experiment - design and cost implications
• Installation and implementation of informatic and analytical software
• Introduction to high-throughput sequencing data analysis
• Reverse engineering gene networks – systems approaches
• Introduction to functional analysis

Centre for Genomic Research, University of Liverpool 

The course is presented by the Centre for Genomic Research at the University of Liverpool in collaboration with the University of Sheffield and funded by the Physiological Society.

We offer keynote talks by experts in the areas covered and a large portion of the course comprises practical computer sessions, allowing delegates to obtain hands-on experience.

This course is designed to provide a 4-day introduction to the conceptual, practical and interpretational issues involved in large-scale gene expression profiling. 

This course covers aspects associated with next-generation sequencing-based approaches to transcriptional profiling (RNA-Seq), comprising the following sections:

• Opportunities presented by genome-wide expression profiling
• Microarray technologies based on cDNA and oligonucleotides
• Sequencing-based approaches to transcript abundance
• Designing a gene expression experiment, microarray and RNAseq
• Analysis of Affymetrix microarray data
• Enrichment analysis of pathways and process