Date & Times
The workshop will be held over two days on Tuesday 25th and Thursday 27th November, 10am-4pm, with registration opening 9.30am on Tuesday.
Description
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 Illumina shotgun metagenomic sequencing data from stool samples to compare Western and Korean diets.
Sessions will start with a brief presentation followed by self-paced computer practicals guided by an online interactive book. The book will contain theory and practice code. Multiple choice questions will guide the interpretation of results.
At the end of the course learners will be able to:
- Carry out quality control of sequencing data, including host removal.
- Explain how Kraken2 utilises k-mers to taxonomically classify sequence data.
- Quantify taxonomic composition of shotgun metagenomic data with Kraken2 & Bracken.
- View taxonomic abundances with Krona.
- Utilise LEfSe for biomarker detection.
- Profile the microbial pathways in metagenomic sequencing data with the bioBakery suite of tools, including HUMAnN.
- Perform a metagenome assembly with MEGAHIT, and assess it with QUAST.
- Carry out genomic binning of the metagenome assembly with MetaBAT2 to try to separate the different species present.
- Functional annotation of the bins with Bakta.
Who is this workshop for
This workshop is aimed at microbiome innovators with a biology background who are interested in analysing the microbial DNA in microbiome and other environmental samples. The workshop contents are planned with beginners to bioinformatics in mind. One week before the workshop, precourse materials for an Intro to Linux workshop will be provided with a computing environment. This will allow attendees without prior linux/bash experience to gain these skills prior to the workshop. If in doubt please send an email to Matthew Gemmell (mgemmell@liverpool.ac.uk).
Contents & timetable
For a breakdown on what will be covered in the sessions please see the agenda.
Eligibility and Application deadline
This course is open to microbiome innovators with a biology background who are interested in analysing the microbial DNA in microbiome and other environmental samples. Places are limited to two individuals per company. Applicants are welcome from across the UK, though priority will be given to companies who have a presence in Liverpool City Region. This deadline to apply is Friday 7th November . After this date applicants will be chosen and emailed to confirm their place on Monday 10th November and asked to confirm their place by Friday 14th November.
Price
The cost of this course is covered by the MAID project
Computer access
Attendees will require their own computer with Zoom and Slack to join the online workshop. The workshop materials are hosted on a website and so no printing is required. The workshop computing environment to be used will be accessed through your web browser via a virtual computer we host. A link to the virtual computer will be sent to confirmed applicants the week before the workshop.
Contacts
If you have a query about your suitability of the workshop, its contents, running of the workshop or payment please email Matthew Gemmell (mgemmell@liverpool.ac.uk)
Feedback from previous attendees
I enjoyed the self-paced learning method very much. I was not rushing to learn too much in one go. I could ask for help whenever needed, which was great.
The instructors were all fantastic, very good at explaining and patient. Thank you!
I really like the format of the workshop and the encouragement to work at our own pace. The workbook is also very clear and really helped me understand how I would apply this to my own data.
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