cloudSPAdes: assembly of synthetic long reads using de Bruijn graphs

Tolstoganov, Ivan; Chen, Zhoutao; Pevzner, Pavel A.

doi:10.1093/bioinformatics/btz349

Cited by 29 publications

(59 citation statements)

References 31 publications

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“…Owing to the high sequence error rate of ONT reads, we found that the accuracy (included the ratio of mapped reads, genomic completeness, single-base accuracy, and structural accuracy) of the Unicycler hybrid assembly based on the NGS assembly contigs was much higher than that of Canu, especially for bacteria with abnormally high GC content. Similar studies used 10X Genomics long-read cloud sequencing data to assemble microbial genomes ( Bishara et al., 2018a , 2018b ; Tolstoganov et al., 2019 ; Weisenfeld et al., 2017 ). We optimized the conditions for the stLFR library construction and sequencing of bacterial genomes and constructed an stLFR de novo assembly pipeline to obtain chromosome-scale bacterial genomes.…”

Section: Discussionmentioning

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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Section: Discussionmentioning

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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“…We refer to the set of reads that share a 3 barcode as a read cloud. The aptly named linked-read technology balances coverage with cost, and is ideally applicable to the problems of metagenomic assembly and structural variant detection [3,24,12].…”

Section: Introductionmentioning

confidence: 99%

Ariadne: Synthetic Long Read Deconvolution Using Assembly Graphs

Meleshko

et al. 2021

Preprint

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Background: De novo assemblies are critical for capturing the genetic composition of complex samples. Linked-read sequencing techniques such as 10x Genomics' Linked-Reads, UST's TELL-Seq, Loop Genomics' LoopSeq, and BGI's Long Fragment Read combines 30 barcoding with standard short-read sequencing to expand the range of linkage resolution from hundreds to tens of thousands of base-pairs. The application of linked-read sequencing to genome assembly has demonstrated that barcoding-based technologies balance the ffs between long-range linkage, per-base coverage, and costs. Linkedreads come with their own challenges, chief among them the association of multiple long fragments with the same 30 barcode. The lack of a unique correspondence between a long fragment and a barcode, in conjunction with low sequencing depth, confounds the assignment of linkage between short-reads. Results: We introduce Ariadne, a novel linked-read deconvolution algorithm based on assembly graphs, that can be used to extract single-species read-sets from a large linked-read dataset. Ariadne deconvolution of linked-read clouds increases the proportion of read clouds containing only reads from a single fragment by up to 37.5-fold. Using these enhanced read clouds in de novo assembly significantly improves assembly contiguity and the size of the largest aligned blocks in comparison to the non-deconvolved read clouds. Integrating barcode deconvolution tools, such as Ariadne, into the postprocessing pipeline for linked-read technologies increases the quality of de novo assembly for complex populations, such as microbiomes. Ariadne is intuitive, computationally efficient, and scalable to other large-scale linked-read problems, such as human genome phasing.

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“…The 10X technology described above is one example of a general approach called synthetic long reads (SLRs), in which the low cost and high accuracy of short reads are combined with long range information provided by a barcoding scheme. Besides 10X Genomics, such technologies are commercialized by Illumina, Loop Genomics and Universal Sequencing Technology [18]. Such linked reads make it possible to assemble repetitive genomic regions as well as reconstruct long haplotype blocks.…”

Section: Introductionmentioning

confidence: 99%

Hap10: reconstructing accurate and long polyploid haplotypes using linked reads

2020

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Background: Haplotype information is essential for many genetic and genomic analyses, including genotype-phenotype associations in human, animals and plants. Haplotype assembly is a method for reconstructing haplotypes from DNA sequencing reads. By the advent of new sequencing technologies, new algorithms are needed to ensure long and accurate haplotypes. While a few linked-read haplotype assembly algorithms are available for diploid genomes, to the best of our knowledge, no algorithms have yet been proposed for polyploids specifically exploiting linked reads. Results: The first haplotyping algorithm designed for linked reads generated from a polyploid genome is presented, built on a typical short-read haplotyping method, SDhaP. Using the input aligned reads and called variants, the haplotype-relevant information is extracted. Next, reads with the same barcodes are combined to produce molecule-specific fragments. Then, these fragments are clustered into strongly connected components which are then used as input of a haplotype assembly core in order to estimate accurate and long haplotypes. Conclusions: Hap10 is a novel algorithm for haplotype assembly of polyploid genomes using linked reads. The performance of the algorithms is evaluated in a number of simulation scenarios and its applicability is demonstrated on a real dataset of sweet potato.

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cloudSPAdes: assembly of synthetic long reads using de Bruijn graphs

Cited by 29 publications

References 31 publications

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

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

Ariadne: Synthetic Long Read Deconvolution Using Assembly Graphs

Hap10: reconstructing accurate and long polyploid haplotypes using linked reads

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