SGTK: a toolkit for visualization and assessment of scaffold graphs

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.