Command line tools for quality control

  • Options can be long and short
  • Structure of a shell command
  • We have confirmed fastp and fastqe are installed
  • The case study and location of the data

The FASTQ format and FASTQE

  • The options available for fastqe
  • The formula for Q scores
  • FASTQE maps scores to emoji
  • FASTQE can be used to quickly asses the quality of sequencing data

Filtering with fastp

  • fastp can be used to filter low quality reads from sequencing data
  • Filtering can improve the quality of data and downstream analysis
  • Emoji can be useful!