hands-on tutorial

Find where a genome is poorly covered, in your browser

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A 20-minute hands-on tutorial: compute coverage and per-position depth with samtools and list low-coverage regions with gawk, using an amplicon run with one failed amplicon, all in the browser.

Licence: Creative Commons Attribution 4.0 International

Keywords: amplicon dropout, coverage, gawk, samtools, sequencing depth, workflow

Competency level: • Beginner

Resource type: hands-on tutorial

Learning objectives:

  • Get the depth at every position with samtools depth
  • Spot an amplicon that failed
  • Summarise coverage with samtools coverage
  • Turn a long table into a short answer with gawk

Authors: IEETA, University of Aveiro

External resources:
BioChef
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