BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files.

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 visualize 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,

SUBMITTER: Payne A 

PROVIDER: S-EPMC6596899 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature