Assembly of long error-prone reads using de Bruijn graphs
By Yu Lin, Jeffrey Yuan, Mikhail Kolmogorov, Max W. Shen, Pavel A. Pevzner. Proceedings of the National Academy of Sciences of the United States of America, 2016
359 citations recorded by the source corpus.
Significance When the long reads generated using single-molecule se-quencing (SMS) technology were made available, most researchers were skeptical about the ability of existing algorithms to generate high-quality assemblies from long error-prone reads. Nevertheless, recent algorithmic breakthroughs resulted in many successful SMS sequencing projects. However, as the recent assemblies of important plant pathogens illustrate, the problem of assembling long error-prone reads is far from being resolved even in the case of relatively short bacterial genomes. We propose an algorithmic approach for assembling long error-prone reads and describe the ABruijn assembler, which results in accurate genome reconstructions. The recent breakthroughs in assembling long error-prone reads were based on the overlap-layout-consensus (OLC) approach and did not utilize the strengths of the alternative de Bruijn graph approach to genome assembly. Moreover, these studies often assume that applications of the de Bruijn graph approach are limited to short and accurate reads and that the OLC approach is the only practical paradigm for assembling long error-prone reads. We show how to generalize de Bruijn graphs for assembling long error-prone reads and describe the ABruijn assembler, which combines the de Bruijn graph and the OLC approaches and results in accurate genome reconstructions.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/08feaa9d17eb1970afd7769d9cf4bc0fc190efcd
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In Molecular Biology
- Mikhail Kolmogorov
- Jeffrey Yuan
- Yu Lin
- Pavel A. Pevzner
- Glenn Tesler
- Steven L. Salzberg
- Mihai Pop
- Sergey Koren
Citations in the corpus
- Assembly of long, error-prone reads using repeat graphs (2018, methodology): “To make a fair comparison, we ran the ABruijn contig-polishing module 6 on the Miniasm output to improve the accuracy of its contigs (referred to as Miniasm + ABruijn).”