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Cloud-SPAN course: Metagenomics

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Cloud-SPAN course: Metagenomics

Denis Barclay

Denis Barclay

Communications Officer

Posted on 7 September 2023

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Cloud-SPAN course: Metagenomics

Posted by d.barclay on 7 September 2023 - 11:45am

Cloud-SPAN logo, free course on metagenomicsCloud-SPAN will host a free course on metagenomics from Monday 6, until Friday 24 November 2023. 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.

The deadline to submit your application is Wednesday, 18 October. The registration form can be accessed here.

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 scholarships to enable members of underrepresented groups and those with financial difficulties to participate in our training courses. For further details, please visit the Clouud-SPAN website

If you have any questions contact cloud-span-project@york.ac.uk or follow  @Spancloud

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