Journal article

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

Son Hoang Nguyen, Minh Duc Cao, Lachlan JM Coin

PLOS COMPUTATIONAL BIOLOGY | PUBLIC LIBRARY SCIENCE | Published : 2021

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 is..

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University of Melbourne Researchers

Grants

Awarded by Australian Research council


Funding Acknowledgements

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.