Nanopore sequencing

Nanopore sequencing has several properties that make it well-suited for our purposes

1. Long-read sequencing technology offers simplified and less ambiguous genome assembly
2. Long-read sequencing gives the ability to span repetitive genomic regions
3. Long-read sequencing makes it possible to identify large structural variations

When using Oxford Nanopore Technologies (ONT) sequencing, the change in electrical current is measured over the membrane of a flow cell. When nucleotides pass the pores in the flow cell the current change is translated (basecalled) to nucleotides by a basecaller. A schematic overview is given in the picture above.

When sequencing using a MinIT or MinION Mk1C, the basecalling software is present on the devices. With basecalling the electrical signals are translated to bases (A,T,G,C) with a quality score per base. The sequenced DNA strand will be basecalled and this will form one read. Multiple reads will be stored in a fastq file.

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