Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information

Chen, Zhoutao; Pham, Long; Wu, Tsai-Chin; Mo, Guoya; Xia, Yu; Chang, Peter L.; Porter, Devin; Phan, Truong Khoa; Che, Huu; Trần, Hợp; Bansal, Vikas; Shaffer, Justin P.; Belda-Ferre, Pedro; Humphrey, Greg; Knight, Rob; Pevzner, Pavel A.; Pham, Son; Wang, Yong; Lei, Ming

doi:10.1101/gr.260380.119

Cited by 91 publications

(121 citation statements)

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“…10x Genomics popularized this technology [1], but since discontinued the sales of their Linked-Reads product lines. However, large volumes of data were produced and still need to be properly analyzed, and other technologies such as TELL-Seq [2] and Haplotagging [3] emerged, and also allow the sequencing of Linked-Reads.…”

Section: Introductionmentioning

confidence: 99%

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LEVIATHAN: efficient discovery of large structural variants by leveraging long-range information from Linked-Reads data

Morisse

Legeai

Lemaitre

2021

Preprint

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Linked-Reads technologies, popularized by 10x Genomics, combine the high- quality and low cost of short-reads sequencing with a long-range information by adding barcodes that tag reads originating from the same long DNA fragment. Thanks to their high-quality and long-range information, such reads are thus particularly useful for various applications such as genome scaffolding and structural variant calling. As a result, multiple structural variant calling methods were developed within the last few years. However, these methods were mainly tested on human data, and do not run well on non-human organisms, for which reference genomes are highly fragmented, or sequencing data display high levels of heterozygosity. Moreover, even on human data, most tools still require large amounts of computing resources. We present LEVIATHAN, a new structural variant calling tool that aims to address these issues, and especially better scale and apply to a wide variety of organisms. Our method relies on a barcode index, that allows to quickly compare the similarity of all possible pairs of regions in terms of amount of common barcodes. Region pairs sharing a sufficient number of barcodes are then considered as potential structural variants, and complementary, classical short reads methods are applied to further refine the breakpoint coordinates. Our experiments on simulated data underline that our method compares well to the state-of-the-art, both in terms of recall and precision, and also in terms of resource consumption. Moreover, LEVIATHAN was successfully applied to a real dataset from a non-model organism, while all other tools either failed to run or required unreasonable amounts of resources. LEVIATHAN is implemented in C++, supported on Linux platforms, and available under AGPL-3.0 License at https://github.com/morispi/LEVIATHAN.

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Section: Introductionmentioning

confidence: 99%

“…Results reported by the different SV calling tools on the two simulated datasets. 1 GROC-SVs crashed after 6 hours 2. LinkedSV crashed after 19 minutes.…”

mentioning

confidence: 99%

LEVIATHAN: efficient discovery of large structural variants by leveraging long-range information from Linked-Reads data

Morisse

Legeai

Lemaitre

2021

Preprint

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“…The use of microbeads as miniaturized virtual compartments allows a practically unlimited number of clonal barcodes to be used per sample at a negligible cost. The stLFR method enables short-read NGS systems to generate highly accurate and economical long-read sequencing information for de novo genome assembly ( Chen et al., 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Comparison of different sequencing strategies for assembling chromosome-level genomes of extremophiles with variable GC content

Zhang

Liu²,

Chen

et al. 2021

iScience

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Summary In this study, six bacterial isolates with variable GC, including Escherichia coli as mesophilic reference strain, were selected to compare hybrid assembly strategies based on next-generation sequencing (NGS) of short reads, single-tube long-fragment reads (stLFR) sequencing, and Oxford Nanopore Technologies (ONT) sequencing platforms. We obtained the complete genomes using the hybrid assembler Unicycler based on the NGS and ONT reads; others were de novo assembled using NGS, stLFR, and ONT reads by using different strategies. The contiguity, accuracy, completeness, sequencing costs, and DNA material requirements of the investigated strategies were compared systematically. Although all sequencing data could be assembled into accurate whole-genome sequences, the stLFR sequencing data yield a scaffold with more contiguity with more completeness of gene function than NGS sequencing assemblies. Our research provides a low-cost chromosome-level genome assembly strategy for large-scale sequencing of extremophile genomes with different GC contents.

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“…Emergent single-molecule sequencing approaches that barcode short reads derived from long DNA fragments up to 50 kb (i.e., linked-reads) ( Zheng et al. 2016 ; Chen et al. 2020 ; Wang et al.…”

Section: Introductionmentioning

confidence: 99%

Reconstruction of Microbial Haplotypes by Integration of Statistical and Physical Linkage in Scaffolding

Cao

Mak

et al. 2021

Molecular Biology and Evolution

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DNA sequencing technologies provide unprecedented opportunities to analyze within-host evolution of microorganism populations. Often, within-host populations are analyzed via pooled sequencing of the population, which contains multiple individuals or ‘haplotypes’. However, current next-generation sequencing instruments, in conjunction with single-molecule barcoded linked-reads, cannot distinguish long haplotypes directly. Computational reconstruction of haplotypes from pooled sequencing has been attempted in virology, bacterial genomics, metagenomics and human genetics, using algorithms based on either cross-host genetic sharing or within-host genomic reads. Here we describe PoolHapX, a flexible computational approach that integrates information from both genetic sharing and genomic sequencing. We demonstrated that PoolHapX outperforms state-of-the-art tools tailored to specific organismal systems, and is robust to within-host evolution. Importantly, together with barcoded linked-reads, PoolHapX can infer whole-chromosome-scale haplotypes from 50 pools each containing 12 different haplotypes. By analyzing real data, we uncovered dynamic variations in the evolutionary processes of within-patient HIV populations previously unobserved in single position-based analysis.

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Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information

Abstract: information generate highly accurate and economical long-range sequencing short-read second-generation sequencing systems to routinely Ultralow-input single-tube linked-read library method enables

Cited by 91 publications

References 40 publications

LEVIATHAN: efficient discovery of large structural variants by leveraging long-range information from Linked-Reads data

LEVIATHAN: efficient discovery of large structural variants by leveraging long-range information from Linked-Reads data

Comparison of different sequencing strategies for assembling chromosome-level genomes of extremophiles with variable GC content

Reconstruction of Microbial Haplotypes by Integration of Statistical and Physical Linkage in Scaffolding

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