Nanopore Sequencing Techniques: A Comparison of the MinKNOW and the Alignator Sequencers

Sebastian Oeck; Alicia I Tüns; Alexander Schramm

doi:10.1007/978-1-0716-3072-3_10

Nanopore Sequencing Techniques: A Comparison of the MinKNOW and the Alignator Sequencers

Methods Mol Biol. 2023:2649:209-221. doi: 10.1007/978-1-0716-3072-3_10.

Authors

Sebastian Oeck¹, Alicia I Tüns², Alexander Schramm²

Affiliations

¹ Department of Medical Oncology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany. sebastian.oeck@uk-essen.de.
² Department of Medical Oncology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.

PMID: 37258864
DOI: 10.1007/978-1-0716-3072-3_10

Abstract

Whole genome and transcriptome analyses represent powerful tools. Despite improvements in sequencing methodology, whole transcriptome analyses are still tedious, especially for methodologies producing long reads. Here, we compare the sequence data analysis software MinKNOW and our tool Alignator. Furthermore, we provide a walk-through from RNA isolation and preparation for MinION sequencing as well as insides in the processing of sequencing data using both tools.

Keywords: Alignator; Alignment; Index; Long reads; MinKNOW; Oxford Nanopore Technology; Sequencing tool.

MeSH terms

Genome
High-Throughput Nucleotide Sequencing / methods
Nanopore Sequencing*
Nanopores*
Sequence Analysis, DNA / methods
Software