James Ferguson

Squiggle adventures with nanopore sequencing

The raw current level data underlying nanopore sequencing technology has been a treasure trove of richer information when hunting for modifications, higher accuracy, or troubleshooting molecular oddities. However, the management and access of this data is not very simple or straightforward. SquiggleKit was developed to demonstrate and provide tools to allow users to investigate this data, how to apply algorithms such as structural segmentation and motif identification, as well as file management and manipulation. Deeplexicon builds on these systems by introducing direct RNA barcoding and demultiplexing utilising signal to image conversion and a deep learning model. Furthermore, FAST5 files have inherent limitations when it comes to data processing and storage, so we created a new nanopore signal specific file format, SLOW5, and associated slow5tools/slow5lib to replace FAST5. It is with these tools we hope to help users create new methods predicated on signal analysis.

Mr James Ferguson

Genomic Systems Analyst, Garvan Institute of Medical Research

James Ferguson is a Genomic Systems Analyst at the Garvan Institute with a background in clinical pathology testing, algorithms, and software development. Leading computational development within the Genomic Technologies Group at the Kinghorn Centre for Clinical Genomics, James applies his unique skills to develop new bioinformatic tools, as well as design and support nanopore sequencing infrastructure.