Assembly of long, error-prone reads using repeat graphs

• Published in: Nature biotechnology Vol. 37; no. 5; pp. 540 - 546
• Main Authors: Kolmogorov, Mikhail, Yuan, Jeffrey, Lin, Yu, Pevzner, Pavel A.
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.05.2019; Nature Publishing Group
• Subjects: 631/114; 631/114/2785/2302; 631/1647/794; 631/208/726; Agriculture; Algorithms; Assemblies; Assembly; Benchmarking; Bioinformatics; Biomedical and Life Sciences; Biomedical Engineering/Biotechnology; Biomedicine; Biotechnology; DNA sequencing; Gene sequencing; Genetic research; Genome, Bacterial - genetics; Genome, Human - genetics; Genomes; Genomics; Genomics - methods; Graphic methods; High-Throughput Nucleotide Sequencing; Human genome; Humans; Life Sciences; Methods; Molecular Sequence Annotation; Repetitive Sequences, Nucleic Acid - genetics; Sequence Analysis, DNA; Software
• ISSN: 1087-0156; 1546-1696; 1546-1696
• DOI: 10.1038/s41587-019-0072-8

Accurate genome assembly is hampered by repetitive regions. Although long single molecule sequencing reads are better able to resolve genomic repeats than short-read data, most long-read assembly algorithms do not provide the repeat characterization necessary for producing optimal assemblies. Here, we present Flye, a long-read assembly algorithm that generates arbitrary paths in an unknown repeat graph, called disjointigs, and constructs an accurate repeat graph from these error-riddled disjointigs. We benchmark Flye against five state-of-the-art assemblers and show that it generates better or comparable assemblies, while being an order of magnitude faster. Flye nearly doubled the contiguity of the human genome assembly (as measured by the NGA50 assembly quality metric) compared with existing assemblers. Flye improves the speed and accuracy of genome assembly by using repeat graphs to resolve repeat regions.