Date: 8 - 10 April 2025

Timezone: London

Language of instruction: English

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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.

Places are restricted to UK-based researchers and only 30 places are available so please only register if you intend on attending.

The workshop will be held over two days on Tuesday 8th and Thursday 10th April 2025, 10am-4pm, with registration opening 9.30am on Tuesday.

The deadline to register is Monday 24th March 2025 noon, 2 weeks before the course. You will hear later that week whether you have been invited and will need to confirm your attendance.

Register to NEOF mailing list to hear first about future NEOF free bioinformatics courses: https://neof.org.uk/news/

City: Online

Country: United Kingdom

Learning objectives:

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 annotate the bins with Prokka.

Organizer: NEOF

Event types:

  • Workshops and courses

Sponsors: NERC


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