Upcoming courses
Metagenomics explores all the genetic material in an environmental sample. It can be used to characterise the taxonomic characteristics of microbial communities.
This online module will be delivered over a three-week period from Monday 6th to Friday 24th November 2023.
Metagenomics analyses involve a lot of data and can take hours to days to complete! But don't worry! The format of the workshop takes account of this. For longer analyses there will be scheduled online zoom sessions to cover concepts and get started followed by offline time for the analysis run and for you to complete some exercises. These will be supported by online drop-ins and a Slack channel for trouble-shooting.
Target audience
UK based Environmental Science researchers at any career stage or anyone with an interest in Metagenomics. We assume no prior experience of the command line or high performance computing. Due to our funding, we prioritise places to researchers within the NERC remit.
Check out testimonials from previous attendees!
💬 This course was fantastic in both helping me to understand the concepts behind metagenomic polishing/assembly processes and in actually learning how to do it ourselves. I have learnt a lot that I can confidently go and apply to my own research.
💬 Really recommend this course! The content was great, covering command line fundamentals and the whole metagenomics workflow in a way that was really easy to understand. The team were super engaged and helpful throughout!
💬 Really pleased with how the course was ran. The instructors were clear and patient, and the online course materials were thorough. I really enjoyed the taxonomic analysis as it brought everything we learned together. This course is super applicable for when I collect and analyse my data further into my PhD project. :)
Registration
There are 30 places available for this online workshop, please register using the online form. Priority will be given to NERC funded students and researchers, as well as researchers from underrepresented groups, although we encourage everyone to apply. This course is free of charge.
Application deadline: 12pm Wednesday 18th October. Applicants will be notified by Monday 23rd October if they have been allocated a place. Scholarships and funding for headsets and monitors will be available.
Programme
We start by teaching the essential tools used in High Performance computing such as file systems and the command-line to connect to and use cloud computing for file navigation and script writing. We then introduce metagenomics and building a metagenomic assembly. In the second week, you will learn how to improve your assembly by ‘polishing’, separate your assembled metagenome into individual genomes (MAGS) and conduct taxonomic assignment and analysis.
But if you can't get something to work, we have a Slack channel and a weekly drop-in to help.
Win £25 in Amazon vouchers for showing commitment to your learning!
At Cloud-SPAN we know it's difficult to find time to train so we've come up with a little incentive for learners signed up for the online course! For the Metagenomics course there will be a prize draw and two people will win a £25 Amazon voucher! All you have to do to enter the prize draw is go through the exercises - we will use your command history to verify your efforts. It doesn't matter if you make mistakes or can't get something to work, it is your commitment that matters!
Happy learning!
Programme
Week 1
Monday 6th November || 1400 - 1600 Introduction. Command-line programming: File systems, files and directories.
Tuesday 7th November || 1400 - 1600 Command-line programming: Using the command line.
Thursday 9th November || 1000 -1330 An introduction to metagenomics, Quality Control and Assembly. Offline time for the assembly to complete.
Week 2
Monday 13th November || 1400-1500 Online troubleshooting drop-in session (optional).
Wednesday 15th November || 1000 - 1130 Polishing your metagenome assembly. Offline time for the polishing to complete.
Friday November 17th || 1400 - 1500 Online troubleshooting drop-in session (optional).
Week 3
Tuesday 21st November || 1000 - 1130 Binning a metagenome assembly into individual genomes (MAGS). Offline time for the binning to complete.
Thursday 23rd November || 1000 - 1100 Online troubleshooting drop-in session (optional).
Friday 24th November || 1300 -1600 Taxonomic Assignment and Analysis.
If you are unable to attend an online session, recordings will be distributed. You will have access to your instance until Friday 1 December (one week after the course is completed) to give you time to consolidate your learning. Usage of the instances will be monitored; instances which are inactive will be closed down as a daily charge is incurred.
We recommend workshop participants have a second monitor and a headset. Dual monitors allow you to engage with the trainers, view materials shared on screen and other participants on one monitor while doing the activities on another. To support you with your learning we have funding to provide you with a headset and a monitor if you require this. To request this additional funding please indicate this in the registration form. Funds for the monitors and headsets will be distributed at the end of course to those participants who regularly attended the online sessions.
Pre-requisites
You will need familiarity with biological concepts, including the concept of microbiome. We assume no prior experience of command line or high performance computing. We assume no prior experience of the command line or high performance computing. Windows users will need to install GitBash.
You don't need to worry about installing metagenomics software or putting the data on your own computer! You will have access to an Amazon Web Services instance with all the data and software and will only need to log in to it.
Learning outcomes
Following completion of this course, learners will be able to:
explain the hierarchical structure of a file system and describe the files and file structure used in the course
explain what is meant by a working directory, a path and a relative path and write down paths that they will need for the course
start a Terminal (Mac) or Git Bash Terminal (Windows)
navigate a file system using the command line
log in to and exit their AWS instance (the cloud)
use common commands such as ls, pwd and cd, on the command line
know the difference between genomics and metagenomics
describe the steps in a metagenomic workflow
perform quality control on reads and assemble them into a metagenome
perform polishing to improve an assembly
use binning to separate the metagenome into different species or MAGs (Metagenome-Assembled Genomes)
use Kraken 2 to assign taxonomy to reads and contigs and phyloseq in R to analyse taxonomic diversity
Scholarships and additional support
We recommend workshop participants have a second monitor and a headset. Dual monitors allow you to engage with the trainers, view materials shared on screen and other participants on one monitor while doing the activities on another. To support you with your learning we have funding to provide you with a headset and a monitor if you require this. To request this additional funding please indicate this in the registration form. Funds for the monitors and headsets will be distributed at the end of course to those participants who regularly attended the online sessions.
We offer scholarships to enable members of underrepresented groups and those with financial difficulties to participate in our training courses. Please complete the relevant section in the application form before 12pm on Wednesday 18th October.
Join us for a Code Retreat!
Our next Code Retreats will take place 12 till 3 pm on Friday 8th December 2023 and 11:00 am till 2pm Tuesday 16th January 2024 at the University of York. Our instructors will be on hand to help you problem-solve the issues that arise as you work. Lunch will be provided and funding is available to support travel to the Code Retreat.
Cloud-SPAN Alumni contact cloud-span-project@york.ac.uk to register and invitations will be distributed shortly.
What could you achieve?
Working with your peers and with help from our instructors, you could:
Revise our Metagenomics course
Get help organising and documenting your own analysis
Apply tools taught in Metagenomics to your own data
Get help with Creating your own Amazon Web Services instance for Genomics
Network with other genomics researchers
Pre-requisites
Attendees should have completed the a Cloud-SPAN course
Attendees will need to bring their own laptop to this event