Optimal assembly for high throughput shotgun sequencing

Bresler, Guy; Bresler, Ma'ayan; Tse, David

doi:10.1186/1471-2105-14-s5-s18

Cited by 88 publications

(91 citation statements)

References 27 publications

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“…In contrast, the greedy algorithm loads only the "best" (longest) overlaps for each read end into memory. This greedy approach is optimal when the read length is sufficiently long (Bresler et al 2013), and a best overlap graph can be built using just 64 GB of memory for a mammalian genome. However, the greedy algorithm can be misled by repeats that are longer than the overlap length and is therefore prone to mis-assemblies.…”

Section: Best Overlap Graphmentioning

confidence: 99%

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

Koren

Walenz

Berlin³

et al. 2016

Preprint

1,151

1,404

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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

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Section: Best Overlap Graphmentioning

confidence: 99%

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

Koren

Walenz

Berlin³

et al. 2016

Preprint

1,151

1,404

View full text Add to dashboard Cite

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“…Despite these successes, shepherding a genome project through the process of DNA isolation, sequencing and assembly is still a challenge, especially for research groups for whom genomes are a means to another goal rather than the goal itself. For example, because high quality genome assembly relies upon long sequencing reads to bridge repetitive genomic regions (6,8,16,17) and high coverage to circumvent read errors (4,7,12), the stringent DNA isolation requirements (size, quantity and purity) for PacBio sequencing (10) intended for genome assembly are higher than those typically employed. Moreover, at present, the low average read quality produced by PacBio sequencing causes coverage requirements to be at least 50-fold (5,13,15).…”

Section: Introductionmentioning

confidence: 99%

Contiguous and accuratede novoassembly of metazoan genomes with modest long read coverage

Chakraborty¹,

Baldwin-Brown²,

Long³

et al. 2016

Nucleic Acids Res

353

294

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Genome assemblies that are accurate, complete and contiguous are essential for identifying important structural and functional elements of genomes and for identifying genetic variation. Nevertheless, most recent genome assemblies remain incomplete and fragmented. While long molecule sequencing promises to deliver more complete genome assemblies with fewer gaps, concerns about error rates, low yields, stringent DNA requirements and uncertainty about best practices may discourage many investigators from adopting this technology. Here, in conjunction with the platinum standard Drosophila melanogaster reference genome, we analyze recently published long molecule sequencing data to identify what governs completeness and contiguity of genome assemblies. We also present a hybrid meta-assembly approach that achieves remarkable assembly contiguity for both Drosophila and human assemblies with only modest long molecule sequencing coverage. Our results motivate a set of preliminary best practices for obtaining accurate and contiguous assemblies, a ‘missing manual’ that guides key decisions in building high quality de novo genome assemblies, from DNA isolation to polishing the assembly.

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“…Moreover, the question of the minimum coverage required may avail itself to information-theoretical bounds and near-optimal solutions, similar to those established for the assembly problem [59,60].…”

Section: Discussionmentioning

confidence: 99%

Assembly-free and alignment-free sample identification using genome skims

Sarmashghi

Bohmann

Gilbert

et al. 2017

Preprint

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The ability to quickly and inexpensively describe the taxonomic diversity in an environment is critical in this era of rapid climate and biodiversity changes. The currently preferred molecular technique is (meta)barcoding in which taxonomically informative plasmid/mitochondrial markers are sequenced. It is low-cost, and widely used, but has drawbacks. As sequencing costs continue to fall, an alternative approach based on genome-skimming has been proposed. This approach first applies low-pass (100Mb -several Gb per sample) sequencing to voucher and/or query samples and then recovers marker genes and/or organelle genomes computationally. In contrast, we suggest the use of the unassembled sequence data for taxonomic identification using an alignment-free approach based on the k-mer decomposition of the sequencing reads. Our approach is motivated by earlier work that connects genomic distance to the Jaccard index on k-mer collections, but improves upon prior work through a careful modeling of the impact of low-coverage, sequencing error, and other factors on the Jaccard index. Our tool, Skmer, estimates genomic distance between two organisms represented by their k-mer collections obtained from the genome-skims, and uses distance estimates to match a genome-skim query to a reference collection. Skmer shows excellent performance in our simulation studies, and makes the assembly-free approach to genome-skimming a viable alternative to the traditional barcoding. The Skmer software is made publicly available on https://github.com/shahab-sarmashghi/Skmer.git

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Optimal assembly for high throughput shotgun sequencing

Cited by 88 publications

References 27 publications

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

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

Contiguous and accuratede novoassembly of metazoan genomes with modest long read coverage

Assembly-free and alignment-free sample identification using genome skims

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