Full Length 16S rRNA PacBio Sequencing and Bioinformatics Analysis
Register here
Date
8-9 and 15-16 April
10am – 3pm
Venue
Edinburgh Genomics, Ashworth Laboratories,
The Kings Buildings Campus, The University of Edinburgh, EH9 3FL, Scotland, United Kingdom
Places
12
You will be contacted by our finance team for full payment. Once payment is made, your place will be confirmed and full details will be sent by our training team.
Registration fee
£350/£374/£411 (University of Edinburgh/Other University/Industrial employees)
Information
16S rRNA sequencing plays a crucial role in identifying bacterial species in microbial community samples. Recent advancements in PacBio’s long-read technologies now enable high-accuracy sequencing of full-length 16S rRNA genes, capable of obtaining species-level resolution. PacBio’s full-length 16S sequencing is comparable in cost to short-read approaches, making it a very cost-effective approach for complex metagenomics studies requiring species level annotation.
This course will introduce the advantages of PacBio’s 16S rRNA amplicon sequencing and explore the differences between short-read and full-length 16S sequencing in terms of amplicon generation, library preparation, sequencing, data quality and analysis workflows. Particular emphasis will be placed on primer structure and usage for full-length 16S rRNA amplification, different approaches to sample barcoding, including the benefits of PacBio’s Kinnex chemistry for higher throughput studies, and sequence annotation strategies.
Participants will gain hands-on experience in preparing full-length 16S rRNA amplicons, conducting sample quality control, pooling samples, as well as performing data quality controls and metagenomics bioinformatics analysis. The course will be taught using high-quality mock microbial DNA community standards, and participants will also have the opportunity to bring up to four of their own extracted DNA samples for full-length 16S amplification, library preparation, sequencing, and analysis.
Instructors
Jena Dryden – Sequencing Technician
Robert Foster – Sequencing Technician
Caitlin Newman – Sequencing Technician
Helen Ritch – Sequencing Technician
Javier Santoyo-Lopez – Facility Manager
Matthew Arno – Lab Manager
Heleen de Weerd – Bioinformatician
Urmi Trivedi – Bioinformatics Team Leader
Kathryn Campbell – Genomics and Bioinformatics Training Coordinator
Workshop format
This is a hybrid course covering both lab and bioinformatics techniques. Please note the two dates: 8-9 April for lab work, then a small gap to complete sequencing and allow our team to check the data, then the bioinformatics component 15-16 April which will take place online.
If you wish to bring your own samples to process, you should check the quantity of DNA present and ensure there is over 10ng and the concentration is 0.4 ng/µl or above. Ideally this will be checked using a Qubit device; Nanodrop measurements are often unreliable. DNA should be high quality and free of RNA, proteins and extraction contaminants. Bring your samples (maximum of 4 samples) in labelled strip tubes or plates.
Who should attend
Graduates, postgraduates, PIs and anyone interested in 16S sequencing.
Requirements
This course assumes you have a basic familiarity with molecular biology and common lab techniques (e.g. use of a pipette, calculating volumes/concentrations), however extra support can be provided with advance notification. Prior to the course, you will be provided with a health & safety document which must be read and signed before starting in the lab. All lab equipment and reagents will be provided, however you may wish to bring your own note-taking equipment.
In addition, a basic knowledge of computing skills for Linux course and R are highly recommended, if needed we offer additional courses for both topics ahead of this training. If you have limited lab or computing experience, please indicate this on the registration form and we will try to accommodate you.
Topics covered
Lab
- Introduction to PacBio Sequencing
- Library Preparation and SMRTbell ligation
- Edinburgh Genomics Lab Tour
- Library QC
- Revio Loading Demo
- QC Discussion
Bioinformatics
- Introduction to R
- Sequencing results in SMRTlink
- Sequencing QC
- DADA2
- Taxonomic Annotation of data
- Basic data visualisation