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Africa's Response to SARS-CoV-2 sequence analysis: Call for Training - COMBAT-SARS-CoV-2

The Africa CDC, and the South African National Bioinformatics Institute invite those interested in joining free training courses on SARS-CoV-2 genome analysis using the COMBAT-SARS-CoV-2 Workbench. This course is for laboratory personnel involved in SARS-CoV-2 genomic sequencing and bioinformatics and technical support sta?. The courses are sponsored by Africa CDC.

This training will be hands-on. On day 1 (9th July) we will cover the theory of SARS-CoV-2 genome analysis, operation of the COMBAT SARS-CoV-2 Workbench including data upload and management, sequence analysis, metadata management and data export. On the second training day (10th July) the technical architecture of the COMBAT SARS- CoV-2 Workbench and installation of the Workbench in a Linux environment will also be covered, thus those involved in systems administration are urged to attend.

COMBAT-SARS-CoV-2 is a web-based environment for SARS-CoV-2 genomic analysis based on the same IRIDA framework as the COMBAT-TB Workbench and was developed with funding of the South African Medical Research Council, the South African National Research Foundation and the Africa CDC.

Register at: https://forms.gle/CroHcNdMEABhcuhF9 before 6 July 2021

Training Schedule

Time (Central African Time) Topic

9 July

10.00 am Introduction to SARS-CoV-2 sequence analysis
10.30 am
  1. Introduction the COMBAT SARS-CoV-2 Workbench Interface
  2. Running analyses using the Workbench
  3. Interpreting analysis output results
  4. Interpreting the “line list” output
11.30 am Break (30 minutes)
12.00 pm
  1. The PHA4GE contextual data specification
  2. Populating the PHA4GE metadata template
  3. Loading data  and metadata into the Workbench
  4. Downloading data from the Workbench
1.00 pm Break (1 hour)
2.00 pm Hands on practice with the Workbench
4.00 pm Closing (Day 1)
   

10 July

10.00 am
  1. Installing the command line uploader
  2. Preparing and loading data using the command line uploader
10.30 am
  1. Introduction to the COMBAT SARS-CoV-2 Workbench architecture
  2. Installing Docker on Linux
  3. Installing the COMBAT SARS-CoV-2 Workbench on Linux
11.30 am Break (30 minutes)
12.00 pm Hands on practice installing the Workbench (on VMs)
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