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

Abstract

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 on tf-idf weighted 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 PacBio or Oxford Nanopore technologies, and achieves a contig NG50 of greater than 21 Mbp on both human and Drosophila melanogaster PacBio datasets. 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.. CC-BY 4.0 International license peer-reviewed) is the author/funder. It is made available under a

Updated Reference Genome Sequence and Annotation of Mycobacterium bovis AF2122/97

“…Two single-molecule real-time (SMRT) cells were used for an output of 542,585,804 bases, a mean read length of 8,141, and 86× reference coverage. DNA sequencing data sets were analyzed using a combination of de novo assembly [short reads, SOAP denovo (10); long reads, Canu (11)] and nucleotide variant identification methods [short reads, Stampy, SAMtools, and VCFtools (12–14); long reads, Pilon (15); and MUMmer (16)]. This allowed both an update of the genome nucleotide sequence and the identification of genomic regions that had been misassembled, or missed entirely, in the original sequencing project.…”

De novo assembly and phasing of a Korean human genome

“…In total, 190 euchromatic gaps were targeted for gap closure with AK1 assembly. The gaps that could not be closed or extended with the AK1 assembly were subjected to closure through local assembly using Canu 27 or a contiguous subread. Subreads mapped 10 kb upstream or downstream of the gap were chosen for local assembly.…”

deBGR: an efficient and near-exact representation of the weighted de Bruijn graph

“…De Bruijn graphs, and k-mer-based processing in general, have also proven useful, even for long read sequence analysis (Carvalho et al , 2016; Koren et al , 2017; Salmela et al , 2016). …”