Cloud-SPAN course: Metagenomics with High Performance Computing

Posted by d.barclay on 6 March 2023 - 9:30am

Metagenomics with High Performance Computing

Cloud-SPAN will host a free course on metagenomics from Tuesday 11, until Friday 21 April 2023. Metagenomics explores all the genetic material in an environmental sample and can be used to characterise the taxonomic characteristics of microbial communities. 

The course is aimed at environmental scientists who would like to use high performance computing for metagenomics analysis or anyone interested in metagenomics. No previous experience of the command line or HPC is required.

This free course comprises online lectures, regular help drop-in sessions and support via slack. 

Following completion, you will be able to:

  • navigate a file system using the command line
  • log in to and exit your AWS instance (the cloud)
  • use common commands such as ls, pwd and cd, on the command line
  • 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

Cloud-SPAN offers Diversity and Hardship Scholarships to enable members of underrepresented groups and those with financial difficulties to participate in our training courses. For further details, please visit the Cloud-SPAN website.

The course is restricted to UK-based researchers and only 30 places are available. If you wish to attend the course, please use the registration form

If you have any questions contact or follow  @Spancloud

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