James M Ferguson1, Martin A Smith1,2. 1. Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia. 2. St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, NSW, Australia.
Abstract
SUMMARY: The management of raw nanopore sequencing data poses a challenge that must be overcome to facilitate the creation of new bioinformatics algorithms predicated on signal analysis. SquiggleKit is a toolkit for manipulating and interrogating nanopore data that simplifies file handling, data extraction, visualization and signal processing. AVAILABILITY AND IMPLEMENTATION: SquiggleKit is cross platform and freely available from GitHub at (https://github.com/Psy-Fer/SquiggleKit). Detailed documentation can be found at (https://psy-fer.github.io/SquiggleKitDocs/). All tools have been designed to operate in python 2.7+, with minimal additional libraries. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
SUMMARY: The management of raw nanopore sequencing data poses a challenge that must be overcome to facilitate the creation of new bioinformatics algorithms predicated on signal analysis. SquiggleKit is a toolkit for manipulating and interrogating nanopore data that simplifies file handling, data extraction, visualization and signal processing. AVAILABILITY AND IMPLEMENTATION: SquiggleKit is cross platform and freely available from GitHub at (https://github.com/Psy-Fer/SquiggleKit). Detailed documentation can be found at (https://psy-fer.github.io/SquiggleKitDocs/). All tools have been designed to operate in python 2.7+, with minimal additional libraries. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Martin A Smith; Tansel Ersavas; James M Ferguson; Huanle Liu; Morghan C Lucas; Oguzhan Begik; Lilly Bojarski; Kirston Barton; Eva Maria Novoa Journal: Genome Res Date: 2020-09-09 Impact factor: 9.043
Authors: Jessie J-Y Chang; Daniel Rawlinson; Miranda E Pitt; George Taiaroa; Josie Gleeson; Chenxi Zhou; Francesca L Mordant; Ricardo De Paoli-Iseppi; Leon Caly; Damian F J Purcell; Timothy P Stinear; Sarah L Londrigan; Michael B Clark; Deborah A Williamson; Kanta Subbarao; Lachlan J M Coin Journal: Cell Rep Date: 2021-04-23 Impact factor: 9.423