Welcome to the "wiki"-practicals of "Bioinformatics of Long Read Sequencing", ed. Zürich 2018.

Link to the etherpad

Table of content

• Contributors

• Practical Information

  • About this hands-on
  • Course information
  • Learning objectives
  • Reproducibility

• Technical Information

  • Docker
  • Unix

• Introduction

  • Technologies in short
  • File organisation
  • Checkpoint

• Data

  • ONT: fast5
  • PacBio: RSII HDF
  • PacBio: Sequel BAM
  • Quality check
  • Checkpoint

• Genome assembly

  • Introduction
  • Assembly
  • Visualisation
  • Polishing
  • Checkpoint

• Genome assembly assessment

  • Introduction
  • Reference-based methods
  • Quality metrics
  • Contamination
  • Checkpoint

• Long-reads transcriptome

  • Introduction
  • PacBio: IsoSeq pipeline
  • ONT: consensus reads
  • Checkpoint

• Transcriptome assessment

  • Introduction
  • Alignment
  • Reference-based methods
  • Checkpoint

• Acknowledgements

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