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BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files

Payne, Alexander; Holmes, Nadine; Rakyan, Vardhman; Loose, Matthew

Authors

Alexander Payne

Nadine Holmes

Vardhman Rakyan

MATTHEW LOOSE matt.loose@nottingham.ac.uk
Professor of Developmental and Computational Biology



Abstract

Motivation: The Oxford Nanopore Technologies (ONT) MinION is used for sequencing a wide variety of sample types with diverse methods of sample extraction. Nanopore sequencers output FAST5 files containing signal data subsequently base called to FASTQ format. Optionally, ONT devices can collect data from all sequencing channels simultaneously in a bulk FAST5 file enabling inspection of signal in any channel at any point. We sought to visualise this signal to inspect challenging or difficult to sequence samples.
Results: The BulkVis tool can load a bulk FAST5 file and overlays MinKNOW (the software that controls ONT sequencers) classifications on the signal trace and can show mappings to a reference. Users can navigate to a channel and time or, given a FASTQ header from a read, jump to its specific position. BulkVis can export regions as Nanopore base caller compatible reads. Using BulkVis, we find long reads can be incorrectly divided by MinKNOW resulting in single DNA molecules being split into two or more reads. The longest seen to date is 2,272,580 bases in length and reported in eleven consecutive reads. We provide helper scripts that identify and reconstruct split reads given a sequencing summary file and alignment to a reference. We note that incorrect read splitting appears to vary according to input sample type and is more common in ’ultra-long’ read preparations.

Citation

Payne, A., Holmes, N., Rakyan, V., & Loose, M. (2018). BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files. Bioinformatics, 35(13), 2193-2198. https://doi.org/10.1093/bioinformatics/bty841

Journal Article Type Article
Acceptance Date Sep 25, 2018
Publication Date Nov 20, 2018
Deposit Date Oct 15, 2018
Publicly Available Date Jan 17, 2019
Journal Bioinformatics
Print ISSN 1367-4803
Electronic ISSN 1460-2059
Publisher Oxford University Press (OUP)
Peer Reviewed Peer Reviewed
Volume 35
Issue 13
Pages 2193-2198
DOI https://doi.org/10.1093/bioinformatics/bty841
Public URL https://nottingham-repository.worktribe.com/output/1165069
Publisher URL https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty841/5193712

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