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	FAST5 data can be converted to FASTQ via the guppy_basecaller software. guppy_basecaller 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.

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