Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

Genome Research - Tập 27 Số 5 - Trang 722-736 - 2017
Sergey Koren1, Brian Walenz1, Konstantin Berlin2, Jason Miller3, Nicholas H. Bergman4, Adam M. Phillippy1
11Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
22Invincea Incorporated, Fairfax, Virginia 22030, USA
33J. Craig Venter Institute, Rockville, Maryland 20850, USA
44National Biodefense Analysis and Countermeasures Center, Frederick, Maryland 21702, USA

Tóm tắt

Long-read single-molecule sequencing has revolutionized de novo genome assembly and enabled the automated reconstruction of reference-quality genomes. However, given the relatively high error rates of such technologies, efficient and accurate assembly of large repeats and closely related haplotypes remains challenging. We address these issues with Canu, a successor of Celera Assembler that is specifically designed for noisy single-molecule sequences. Canu introduces support for nanopore sequencing, halves depth-of-coverage requirements, and improves assembly continuity while simultaneously reducing runtime by an order of magnitude on large genomes versus Celera Assembler 8.2. These advances result from new overlapping and assembly algorithms, including an adaptive overlapping strategy based ontf-idfweighted MinHash and a sparse assembly graph construction that avoids collapsing diverged repeats and haplotypes. We demonstrate that Canu can reliably assemble complete microbial genomes and near-complete eukaryotic chromosomes using either Pacific Biosciences (PacBio) or Oxford Nanopore technologies and achieves a contig NG50 of >21 Mbp on both human andDrosophila melanogasterPacBio data sets. For assembly structures that cannot be linearly represented, Canu provides graph-based assembly outputs in graphical fragment assembly (GFA) format for analysis or integration with complementary phasing and scaffolding techniques. The combination of such highly resolved assembly graphs with long-range scaffolding information promises the complete and automated assembly of complex genomes.

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Genome Research

Tập 27 Số 5

722-736

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