hands-on tutorial

Analyse amplicon sequencing of a virus in your browser

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A 30-minute hands-on tutorial: map amplicon reads, trim primers and call variants and a consensus with iVar and samtools, all in the browser with nothing to install.

Licence: Creative Commons Attribution 4.0 International

Keywords: amplicon sequencing, genomic surveillance, iVar, primer trimming, virus, workflow

Competency level: •• Intermediate

Resource type: hands-on tutorial

Learning objectives:

  • Build a longer workflow with three inputs
  • Make a pileup and call variants with iVar
  • Tell real variants from sequencing errors by frequency
  • Trim primer sequences from amplicon reads

Authors: IEETA, University of Aveiro

External resources:
BioChef
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