TRAINING

Our expertise and equipment is readily available to researchers from across the UK, and to train those at the start of their careers.

Visitor Facility

We provide year-round bespoke training to researchers who undertake the laboratory and/or analytical components of their project under our supervision at our Visitor Facility (VF) located in the Molecular Ecology Laboratory at the University of Sheffield.
 
We support PhD students, research fellows, PDRAs and research technicians, who are working within the NERC remit. We cannot support Masters or undergraduate students.
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The Visitor Facility was first established in 1998, has been regularly updated, and so is extremely well equipped for all molecular population genetic and genomic applications. Visitors are supervised by the NEOF team but also have the opportunity to participate in seminars and to interact with other members of the Ecology and Evolutionary Biology research cluster. Visits vary in length from days to months.

Access, including consumables, is free to successful applicants (see Eligibility), but we do not support travel and accommodation costs. Users of the Visitor Facility also have free access to the new-generation DNA sequencing that their project requires. While the amount of sequencing is not unlimited, we aim to provide sufficient sequencing to enable users to produce a published output. Potential applicants should initiate a discussion about their proposed project via our enquiry form.

Bioinformatics courses

We provide training courses to support a range of capabilities including, for example, genome assembly, metabarcoding, population genomics and RNA sequencing. We aim to support the training that is in most demand from our community.

These are some of the training courses we are running online in 2021 and 2022. Our plan is to deliver these courses online until further notice, and we hope to be running workshops in person in future.

Registration closes on Monday at noon 2 weeks prior to the start of each course; selected attendees are then invited to confirm their attendance.

 

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Introduction to Command Line bioinformatics - Tue 26 Oct 2021

Bioinformatics is an increasingly important skill for biological scientists. Many bioinformatic tools can only be run on Unix based operating systems. This one day course (10am-4pm) is aimed at beginners and novices to the command line; it will give an overview of fundamental unix commands, directory navigation, and file manipulation. The course will act as a perfect primer for those interested in our other Bioinformatic courses. 

Register via this form.

 

Introduction to R - 9, 11, 16, & 18 November

R is a highly used programming language for visualisation of data and statistical analysis. There are many R packages for the analysis of biological datasets. This course is aimed at beginners and novices to R. It will give an in depth overview of the foundations of R and Rstudio plus introduce data sorting, visualisation and statistical analysis.

Register via this form.

Introduction to sequencing data and quality control - Tue 30 Nov & Thu 2 Dec 2021

There are 3 sequencing technologies that are heavily used for biological research; Illumina, PacBio, and ONT. These three technologies each have their own errors and biases. At the end of this course you will understand these error profiles, and be able to use command line tools to measure sequencing quality and conduct quality control.

Register via this form

Population genomics - Tuesday 25 & Thursday 27 January 2022

This course will introduce participants to a variety of population genomics analyses for large next generation sequencing (NGS) datasets. It will include discussion on single nucleotide polymorphism (SNP) calling and filtering options, an introduction to population genomics statistics, examining genetic structure, and Fst-based analyses such as outlier detection/genomic islands of divergence.

Register via this form

Bacterial 16S metabarcoding - mid February 2022

Sequencing of the 16S rRNA gene is a well established method of determining the bacterial taxonomic composition of microbiomes. This has been used for human and animal body sites, soil, sewage, clouds, deserts, permafrost and many other environments. This course will give you the ability to describe the advantages and disadvantages of 16S rRNA sequencing, and analyse 16S rRNA datasets with the QIIME2 bioinformatics platform.

Metabarcoding for diet analysis and environmental DNA - mid March 2022

Sequencing DNA barcodes from mixed sources of DNA is an increasingly used way to survey biodiversity, whether analysing dietary content from faecal-derived DNA or monitoring aquatic species from water-derived DNA. This course will give an overview of metabarcoding with different barcoding genes to target particular taxa. Using an example data set we will go from raw sequence data through to assigning taxonomy to the sequence variants.

 

Microbial shotgun metagenomics - early April 2022

There are many unknown and unculturable microbes found in a vast array of different environments. Shotgun metagenomics is an approach to capture all the genetic information in a sample, providing the taxonomic and metabolic information of all present organisms. In this course we will analyse shotgun metagenomic sequencing data from stool samples to compare western and Korean diets. At the end of the course you will be able to quantify the taxonomic composition with Kraken2 & Bracken, and determine the metabolic profile with the bioBakery suite of tools.

Registration deadline 24/05.

Introduction to R - mid May 2022

R is a highly used programming language for visualisation of data and statistical analysis. There are many R packages for the analysis of biological datasets. This course is aimed at beginners and novices to R. It will give an in depth overview of the foundations of R and Rstudio plus introduce data sorting, visualisation and statistical analysis.

Bacterial genome assembly and annotation - mid June 2022

With the advent and improvement of long read sequencing technologies, bacterial genome assembly and annotation is easier and more effective than ever. At the end of this course you will be able to perform genome assembly and polishing of PacBio sequencing followed by annotation with prokka. Additionally you will be able to assess the quality of the genome with contiguity measures from QUAST and genome completeness estimation with BUSCO.

RNA-seq gene expression and pathway analysis - mid July 2022

RNA-Seq (AKA whole transcriptomic shotgun sequencing) aims to determine the presence and quantity of RNA in a biological sample at a given moment in time. This allows you to determine the level of expression of these genes and therefore compare these expressions across different sample groups, i.e. Differential Gene Expression (DGE). At the end of this course you will be able to align the transcriptomes of samples to a reference genome to determine gene expression levels. Following this you will be able to carry out Differential Gene Expression analysis to determine which genes are up and down regulated between sample groups.

Eukaryote and large genome assembly and annotation

Many eukaryotic genomes are larger and more complex than bacterial genomes, requiring different tools for optimal genome assembly and annotation. This course will give an overview of long read genome assembly and polishing followed by scaffolding and gap filling. We will then assess the contiguity and completeness of the assembly with QUAST and BUSCO. Finally we will annotate the genome assembly with the annotation pipeline MAKER.

Workshops we have previously run and feedback

I am very thankful to the instructors as this is the first time I have been able to complete AND UNDERSTAND a bioinformatics workshop. The topics covered in this workshop will be very useful and the format allowed me to work at my own pace without worrying that I’m falling behind. I will be signing up to more workshops!

I thoroughly enjoyed this course and it will be directly useful for my own (NERC funded) PhD research. Matthew’s description of the concepts were very clear, and the course leaders also answered all questions very clearly (and they were lovely!). The online format worked smoothly and felt like I was there in person. I look forward to future courses!

The concepts were very well explained at the start and the overall presentation was great. Questions were answered quickly and well detailed.

Another great course, feel like I have a much better understanding of the concepts and I think the work book exercises are great.

Introduction to command line bioinformatics - Tue 23 Feb 2021.

Bioinformatics is an increasingly important skill for biological scientists. Many bioinformatic tools can only be run on Unix based operating systems. This course is aimed at beginners and novices to the command line; it will give an overview of fundamental unix commands, directory navigation, and file manipulation. The course will act as a perfect primer for those interested in our other Bioinformatic courses.

Introduction to sequencing data and quality control - Tue 16 & Thu 18 March 2021

There are 3 sequencing technologies that are heavily used for biological research; Illumina, PacBio, and ONT. These three technologies each have their own errors and biases. At the end of this course you will understand these error profiles, and be able to use command line tools to measure sequencing quality and conduct quality control.

Bacterial 16S metabarcoding - 27 & 29 April 2021
Sequencing of the 16S rRNA gene is a well established method of determining the bacterial taxonomic composition of microbiomes. This has been used for human and animal body sites, soil, sewage, clouds, deserts, permafrost and many other environments. This course will give you the ability to describe the advantages and disadvantages of 16S rRNA sequencing, and analyse 16S rRNA datasets with the QIIME2 bioinformatics platform.
Metabarcoding for diet analysis and environmental DNA - Tue 18 & Thu 20 May 2021

Sequencing DNA barcodes from mixed sources of DNA is an increasingly used way to survey biodiversity, whether analysing dietary content from faecal-derived DNA or monitoring aquatic species from water-derived DNA. This course will give an overview of metabarcoding with different barcoding genes to target particular taxa. Using an example data set we will go from raw sequence data through to assigning taxonomy to the sequence variants.

Microbial shotgun metagenomics - Tue 1 & Thu 3 June 2021

There are many unknown and unculturable microbes found in a vast array of different environments. Shotgun metagenomics is an approach to capture all the genetic information in a sample, providing the taxonomic and metabolic information of all present organisms. In this course we will analyse shotgun metagenomic sequencing data from stool samples to compare western and Korean diets. At the end of the course you will be able to quantify the taxonomic composition with Kraken2 & Bracken, and determine the metabolic profile with the bioBakery suite of tools.

Population genomics - Tue 13 & Thu 15 July 2021

This course will introduce participants to a variety of population genomics analyses for large next generation sequencing (NGS) datasets. It will include discussion on single nucleotide polymorphism (SNP) calling and filtering options, an introduction to population genomics statistics, examining genetic structure, and Fst-based analyses such as outlier detection/genomic islands of divergence.

Bacterial genome assembly and annotation - Tue 24 & Thu 26 Aug 2021

With the advent and improvement of long read sequencing technologies, bacterial genome assembly and annotation is easier and more effective than ever. At the end of this course you will be able to perform genome assembly and polishing of PacBio sequencing followed by annotation with prokka. Additionally you will be able to assess the quality of the genome with contiguity measures from QUAST and genome completeness estimation with BUSCO.

RNA-seq gene expression and pathway analysis - Tue 21 & Thu 23 Sep 2021

RNA-Seq (AKA whole transcriptomic shotgun sequencing) aims to determine the presence and quantity of RNA in a biological sample at a given moment in time. This allows you to determine the level of expression of these genes and therefore compare these expressions across different sample groups, i.e. Differential Gene Expression (DGE). At the end of this course you will be able to align the transcriptomes of samples to a reference genome to determine gene expression levels. Following this you will be able to carry out Differential Gene Expression analysis to determine which genes are up and down regulated between sample groups.

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If you would like more information about NEOF and the services we offer, or make any other enquiry, please complete our form.