The advantages of SMRT sequencing

Roberts, Richard J.; Carneiro, Mauricio O.; Schatz, Michael C.

doi:10.1186/gb-2013-14-6-405

Cited by 542 publications

(395 citation statements)

References 17 publications

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“…Novel technologies such as single-molecule real-time (SMRT) sequencing have been developed [74]. This particular technology has advantages such as the generation of long reads and high accuracy.…”

Section: Groups and Metagenomicsmentioning

confidence: 99%

Biofloc Technology (BFT): A Tool for Water Quality Management in Aquaculture

Emerenciano¹,

Córdova²,

et al. 2017

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Biofloc technology (BFT) is considered the new "blue revolution" in aquaculture. Such technique is based on in situ microorganism production which plays three major roles: (i) maintenance of water quality, by the uptake of nitrogen compounds generating in situ microbial protein; (ii) nutrition, increasing culture feasibility by reducing feed conversion ratio (FCR) and a decrease of feed costs; and (iii) competition with pathogens. The aggregates (bioflocs) are a rich protein-lipid natural source of food available in situ 24 hours per day due to a complex interaction between organic matter, physical substrate, and large range of microorganisms. This natural productivity plays an important role recycling nutrients and maintaining the water quality. The present chapter will discuss some insights of the role of microorganisms in BFT, main water quality parameters, the importance of the correct carbon-to-nitrogen ratio in the culture media, its calculations, and different types, as well as metagenomics of microorganisms and future perspectives.

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Section: Groups and Metagenomicsmentioning

confidence: 99%

Biofloc Technology (BFT): A Tool for Water Quality Management in Aquaculture

Emerenciano¹,

Córdova²,

et al. 2017

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“…The experimental comparison on the real long read dataset is focused on evaluating the accuracy of the tools under the all-heterozygous assumption since such a standard benchmark dataset has low average coverage ($3Â) and contains only heterozygous SNP positions. We also assessed accuracy and performances of the tools while varying coverage, read length and sequencing/indel error rate on simulated long read datasets with characteristics similar to those of the 'futuregeneration' sequencing technologies that are currently (or soon) available (coverage up to 25Â, read length up to 50 000 bases, substitution error rate up to 5% and indel rate equal to 10%) (Carneiro et al, 2012;Jain et al, 2015;Roberts et al, 2013).…”

Section: Resultsmentioning

confidence: 99%

“…These rates reflect the characteristics of the long read data generated by the future-generation sequencing technologies (Carneiro et al, 2012;Jain et al, 2015;Roberts et al, 2013). From each set of simulated reads, five datasets were obtained by randomly extracting a maximal subset with (maximum) coverage of 15Â, 20Â and 25Â.…”

Section: Simulated Datasetsmentioning

confidence: 99%

“…HAPCOL turns out to be competitive with the considered methods, improving the accuracy and the number of phased positions. We also assessed accuracy and performance of HAPCOL on a large collection of realistically simulated datasets reflecting the characteristics of 'future-generation' sequencing technologies that are currently (or soon) available (coverage up to 25Â, read length from 10000 to 50 000 bases, substitution error rate up to 5% and indel rate equal to 10%) (Carneiro et al, 2012;Jain et al, 2015;Roberts et al, 2013). When considering higher coverages, interesting applications such as SNP calling or heterozygous SNPs validation become feasible and reliable (Nielsen et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

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HapCol: accurate and memory-efficient haplotype assembly from long reads

et al. 2015

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Motivation: Haplotype assembly is the computational problem of reconstructing haplotypes in diploid organisms and is of fundamental importance for characterizing the effects of single-nucleotide polymorphisms on the expression of phenotypic traits. Haplotype assembly highly benefits from the advent of 'future-generation' sequencing technologies and their capability to produce long reads at increasing coverage. Existing methods are not able to deal with such data in a fully satisfactory way, either because accuracy or performances degrade as read length and sequencing coverage increase or because they are based on restrictive assumptions. Results: By exploiting a feature of future-generation technologies-the uniform distribution of sequencing errors-we designed an exact algorithm, called HAPCOL, that is exponential in the maximum number of corrections for each single-nucleotide polymorphism position and that minimizes the overall error-correction score. We performed an experimental analysis, comparing HAPCOL with the current state-of-the-art combinatorial methods both on real and simulated data. On a standard benchmark of real data, we show that HAPCOL is competitive with state-of-the-art methods, improving the accuracy and the number of phased positions. Furthermore, experiments on realistically simulated datasets revealed that HAPCOL requires significantly less computing resources, especially memory. Thanks to its computational efficiency, HAPCOL can overcome the limits of previous approaches, allowing to phase datasets with higher coverage and without the traditional all-heterozygous assumption.

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“…This loss of spatial information requires an intensive computational process to reassemble the original DNA sequence. While longer, more contiguous reads do preserve more spatial relatedness and thus improve DNA assembly [5], there is still significant room for improvement, particularly in long repetitive regions.…”

Section: Introductionmentioning

confidence: 99%

Fragmentation of Surface Adsorbed and Aligned DNA Molecules using Soft Lithography for Next-Generation Sequencing

Cho¹,

Goodwin²,

Budassi³

et al. 2017

J Biosens Bioelectron

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In this study, the enzymatic in situ cutting of linearized DNA molecules at approximately 11 kbp intervals is demonstrated using a soft lithography technique. The ultimate goal is to provide a general ordered cutting method to greatly simplify the assembly process. DNA was stretched onto PMMA (Poly methyl methacrylate) coated silicon by withdrawing the substrate from a DNA solution (a process termed "combing"). The stretched lambda DNA could be linearly cut with a soft lithography stamp used to selectively apply DNase I. After cutting the DNA on the substrate, the DNA fragments are removed from the surface by incubating PMMA in the commercial NEBuffer 3.1 at 75°C. The recovered fragments desorbed into the buffer and were sequenced using the PacBio RS II sequencer without an amplification step. The mean coverage was 2870X for the approximately 11 kbp fragmented sample and 100% of the lambda genome was sequenced. Methods to extend of the technique to ordered fragmentation are discussed.

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The advantages of SMRT sequencing

Abstract: Of the current next-generation sequencing technologies, SMRT sequencing is sometimes overlooked. However, attributes such as long reads, modified base detection and high accuracy make SMRT a useful technology and an ideal approach to the complete sequencing of small genomes.

Cited by 542 publications

References 17 publications

Biofloc Technology (BFT): A Tool for Water Quality Management in Aquaculture

Biofloc Technology (BFT): A Tool for Water Quality Management in Aquaculture

HapCol: accurate and memory-efficient haplotype assembly from long reads

Fragmentation of Surface Adsorbed and Aligned DNA Molecules using Soft Lithography for Next-Generation Sequencing

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