Real-time resolution of short-read assembly graph using ONT long reads

Son Hoang Nguyen; Minh Duc Cao; Lachlan J M Coin

doi:10.1371/journal.pcbi.1008586

Real-time resolution of short-read assembly graph using ONT long reads

PLoS Comput Biol. 2021 Jan 20;17(1):e1008586. doi: 10.1371/journal.pcbi.1008586. eCollection 2021 Jan.

Authors

Son Hoang Nguyen¹, Minh Duc Cao¹, Lachlan J M Coin^{1

2

3

4}

Affiliations

¹ Institute for Molecular Bioscience, the University of Queensland, St Lucia, Brisbane, Australia.
² Department of Microbiology and Immunology, The University of Melbourne, Parkville, Australia.
³ Department of Clinical Pathology, The University of Melbourne, Parkville, Australia.
⁴ Department of Infectious Disease, Imperial College London, London, UK.

Abstract

A streaming assembly pipeline utilising real-time Oxford Nanopore Technology (ONT) sequencing data is important for saving sequencing resources and reducing time-to-result. A previous approach implemented in npScarf provided an efficient streaming algorithm for hybrid assembly but was relatively prone to mis-assemblies compared to other graph-based methods. Here we present npGraph, a streaming hybrid assembly tool using the assembly graph instead of the separated pre-assembly contigs. It is able to produce more complete genome assembly by resolving the path finding problem on the assembly graph using long reads as the traversing guide. Application to synthetic and real data from bacterial isolate genomes show improved accuracy while still maintaining a low computational cost. npGraph also provides a graphical user interface (GUI) which provides a real-time visualisation of the progress of assembly. The tool and source code is available at https://github.com/hsnguyen/assembly.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Computational Biology
DNA, Bacterial / analysis
DNA, Bacterial / genetics
Genome, Bacterial / genetics
Nanopores*
Nanotechnology
Sequence Alignment / methods*
Sequence Analysis, DNA / methods*
Software
User-Computer Interface

Substances

DNA, Bacterial

Grants and funding

This study was supported by a Discovery Project with grant number DP170102626 awarded by the Australian Research council to MC and LC. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.