Olga Kunyavskaya1, Andrey D Prjibelski1. 1. Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg 199034, Russia.
Abstract
SUMMARY: Scaffolding is an important step in every genome assembly pipeline, which allows to order contigs into longer sequences using various types of linkage information, such as mate-pair libraries and long reads. In this work, we operate with a notion of a scaffold graph-a graph, vertices of which correspond to the assembled contigs and edges represent connections between them. We present a software package called Scaffold Graph ToolKit that allows to construct and visualize scaffold graphs using different kinds of sequencing data. We show that the scaffold graph appears to be useful for analyzing and assessing genome assemblies, and demonstrate several use cases that can be helpful for both assembly software developers and their users. AVAILABILITY AND IMPLEMENTATION: SGTK is implemented in C++, Python and JavaScript and is freely available at https://github.com/olga24912/SGTK. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
SUMMARY: Scaffolding is an important step in every genome assembly pipeline, which allows to order contigs into longer sequences using various types of linkage information, such as mate-pair libraries and long reads. In this work, we operate with a notion of a scaffold graph-a graph, vertices of which correspond to the assembled contigs and edges represent connections between them. We present a software package called Scaffold Graph ToolKit that allows to construct and visualize scaffold graphs using different kinds of sequencing data. We show that the scaffold graph appears to be useful for analyzing and assessing genome assemblies, and demonstrate several use cases that can be helpful for both assembly software developers and their users. AVAILABILITY AND IMPLEMENTATION: SGTK is implemented in C++, Python and JavaScript and is freely available at https://github.com/olga24912/SGTK. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Jordan M Eizenga; Adam M Novak; Jonas A Sibbesen; Simon Heumos; Ali Ghaffaari; Glenn Hickey; Xian Chang; Josiah D Seaman; Robin Rounthwaite; Jana Ebler; Mikko Rautiainen; Shilpa Garg; Benedict Paten; Tobias Marschall; Jouni Sirén; Erik Garrison Journal: Annu Rev Genomics Hum Genet Date: 2020-05-26 Impact factor: 8.929
Authors: Ting Wang; Lucinda Antonacci-Fulton; Kerstin Howe; Heather A Lawson; Julian K Lucas; Adam M Phillippy; Alice B Popejoy; Mobin Asri; Caryn Carson; Mark J P Chaisson; Xian Chang; Robert Cook-Deegan; Adam L Felsenfeld; Robert S Fulton; Erik P Garrison; Nanibaa' A Garrison; Tina A Graves-Lindsay; Hanlee Ji; Eimear E Kenny; Barbara A Koenig; Daofeng Li; Tobias Marschall; Joshua F McMichael; Adam M Novak; Deepak Purushotham; Valerie A Schneider; Baergen I Schultz; Michael W Smith; Heidi J Sofia; Tsachy Weissman; Paul Flicek; Heng Li; Karen H Miga; Benedict Paten; Erich D Jarvis; Ira M Hall; Evan E Eichler; David Haussler Journal: Nature Date: 2022-04-20 Impact factor: 69.504