James Ferguson from the Garvan Institute of Medical Research in Australia presented at London Calling 2019 on “SquiggleKit: a toolkit for manipulating nanopore signal data.” I had heard about the toolkit from another speaker and session. Ferguson spoke about the history of the toolkit and why they worked to develop SquiggleKit. They created five tools: Fast5_fetcher, SquigglePull, SquigglePlot, Segmenter, and MotifSeq. Ferguson explained how these tools build on and improve others. The tools were developed to be adaptable. Fast5_fetcher filters the sections/sequences you want to obtain in fast5 format. SquigglePull obtains a squiggle, while SquigglePlot allows the user to create nicer plots. Segmenter helps the user obtain segments of a squiggle. MotifSeq is a “Control-F” to find specific sequences in squiggles. There is no compiling, and the toolkit works with various operating systems. Ferguson demonstrated each tool with the syntax needed and output. The toolkit seems user-friendly and powerful. I wonder what we could learn from analyzing squiggle from bacterial genomics and transcriptomics?
