This lesson is still being designed and assembled (Pre-Alpha version)

Nanopore Sequencing: Glossary

Key Points

Nanopore-based sequencing: introduction
  • ONT produce a range of popular sequencing platforms.

  • This technology is constantly advancing.

Data Transfer
  • There are multiple methods to transfer data to and from NeSI.

  • The method of choice depends on the size of the data.

Nanopore - Basecalling
  • POD5/FAST5 data can be converted to BAM or FASTQ via the dorado software.

  • dorado has different models (FAST, HAC and SUP) that provide increasing basecall accuracy (and take increasing amounts of computation).

  • Once bascalling has been done, standard tasks such as QA/QC, mapping and variant calling can be performed.

Nanopore: quality assessment
  • FastQC and NanoPlot provide pre-formatted reports on run characteristics and read quality.

  • Bioawk can be used to generate summary metrics and ask specific questions about the read data.

Nanopore - Variant Calling
  • Long-read based algorithms (e.g., minimap2) need to be used when aligning long read data.

  • Post-alignment, standard software tools (e.g., samtools, bcftools, etc) can be used to perform variant calling.

Nanopore - Adaptive Sampling
  • Nanopore can determine if it should continue to sequence a read.

Glossary

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