Onward analysisĪ range of approaches are available for downstream analysis of nanopore sequencing data, to suit all requirements and levels of bioinformatics expertise.
Research basecallers, such as Bonito, are available on Oxford Nanopore’s GitHub, providing users with access to the latest, high-performance cutting-edge algorithms which are currently in development. Guppy is integrated into MinKNOW and is also available as a standalone version. The Guppy toolkit also performs modified basecalling (5mC, 6mA and CpG) from the raw signal data, producing an additional FAST5 file of modified base probabilities. Guppy, an example of the former, is a data processing toolkit that contains Oxford Nanopore’s basecalling algorithms, and several bioinformatic post-processing features, such as barcoding/demultiplexing, adapter trimming, and alignment. Basecalling and primary data analysisīasecalling can be defined as the process of converting the electrical signals generated by a DNA or RNA strand passing through the nanopore into the corresponding base sequence of the strand.Ī choice of basecalling tools is available, some of which are fully supported and some of which are in development.
FAST5 files contain raw signal data that can be used for basecalling and calling base modifications, such as methylation. MinKNOW produces FAST5 (HDF5) files and/or FASTQ files, according to your preference.
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Adaptive sampling is also incorporated into MinKNOW this is a novel method of targeted sequencing requiring no additional library prep – regions of interest are rejected or accepted in real time by the software itself. MinKNOW, the operating software that drives nanopore sequencing devices, carries out several core tasks, including data acquisition, real-time analysis and run feedback, local basecalling, and data streaming. As detailed on this page, Oxford Nanopore provides solutions at each stage, accommodating all user needs, applications, and levels of bioinformatics expertise. From the moment data acquisition begins, analysis can be The nanopore sequencing analysis workflow is simple and easy to follow: with five steps from raw data acquisition toĪnalysis completion and experimental interpretation. Onboard basecalling with Guppy means that neither a local infrastructure nor a stable internet connection is.Stop sequencing as soon as sufficient data has been obtained.Real-time basecalling, enabling immediate access to results.Nanopore sequencing presents a number of significant advantages which allow the sequencing process to be tailored to Analysis solutions for nanopore sequencing data