Please read the following article and come prepared to discuss.

Rang FJ, Kloosterman WP, De Ridder J (2018). From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy. Genome Biology 19: 90

We will also review some of the following tools.

Quality assessment:

• NanoPlot
• Poretools
• BulkVis
• PycoQC
• MinIONQC
• PyPore

Adapter trimming:

• Porechop

Mapping:

• minimap2

Officially ONT-supported pipelines:

• ont-assembly-polish
• medaka
• pipeline-structural-variation

Methylation calling:

• tombo