Abstract
The revolution of genome sequencing is continuing after the successful second-generation sequencing (SGS) technology. The third-generation sequencing (TGS) technology, led by Pacific Biosciences (PacBio), is progressing rapidly, moving from a technology once only capable of providing data for small genome analysis, or for performing targeted screening, to one that promises high quality de novo assembly and structural variation detection for human-sized genomes. In 2014, the MinION, the first commercial sequencer using nanopore technology, was released by Oxford Nanopore Technologies (ONT). MinION identifies DNA bases by measuring the changes in electrical conductivity generated as DNA strands pass through a biological pore. Its portability, affordability, and speed in data production makes it suitable for real-time applications, the release of the long read sequencer MinION has thus generated much excitement and interest in the genomics community. While de novo genome assemblies can be cheaply produced from SGS data, assembly continuity is often relatively poor, due to the limited ability of short reads to handle long repeats. Assembly quality can be greatly improved by using TGS long reads, since repetitive regions can be easily expanded into using longer sequencing lengths, despite having higher error rates at the base level. The potential of nanopore sequencing has been demonstrated by various studies in genome surveillance at locations where rapid and reliable sequencing is needed, but where resources are limited.
Highlights
The revolution of genome sequencing is continuing after the successful secondgeneration sequencing (SGS) technology
We focus on MinION sequencing, the data characteristics, the algorithms for genome assembly, and the differences between the Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) platforms
The hierarchical genome-assembly process (HGAP) [40] was developed for PacBio long reads with inputs of PacBio-specific h5 files [41], which are different from the signal-level data generated by the MinION device
Summary
The revolution of genome sequencing is continuing after the successful secondgeneration sequencing (SGS) technology. We focus on MinION sequencing, the data characteristics, the algorithms for genome assembly, and the differences between the PacBio and ONT platforms.
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