Benchmarking of next and third generation sequencing technologies and their associated algorithms for <i>de novo</i> genome assembly

Gavrielatos, Marios; Kyriakidis, Konstantinos; Spandidos, Demetrios A.; Michalopoulos, Ioannis

doi:10.3892/mmr.2021.11890

Cited by 23 publications

(18 citation statements)

References 56 publications

(49 reference statements)

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“…Not long ago, the relatively low-throughput, the high error rate, and the cost limited the exploitation of third-generation sequencing in display technologies. The circular consensus reads that the more widespread platforms’ availability is making this paradigm shift overcome challenges with the higher sequencing error rate, and also leads to a reduction in sequencing costs [ 65 ]. The promise of the application of third-generation sequencing is emerging in recent literature, demonstrating that PacBio circumvents the issue of VH and VL matching [ 66 , 67 , 68 ].…”

Section: Discussionmentioning

confidence: 99%

“…The greatest breakthrough in third-generation sequencing was the development of circular consensus sequencing, by which a single molecule can be circularized and sequenced several times to radically reduce the error rate. These technical and bioinformatic improvements have led to obtaining ultra-long (up to 25 kilobases) and increasingly accurate (99.9% for PacBio; 97% for Nanopore) reads [ 49 , 65 ]. The implementation of long accurate reads and the recent introduction of sample multiplexing by barcoding renders the third-generation sequencing platforms very useful to obtain quantitative information of full-length antibody fragments (scFv, Fab) from library screenings.…”

Section: Implementation Of Next Generation Sequencing To Phage Displa...mentioning

confidence: 99%

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High-Throughput Monoclonal Antibody Discovery from Phage Libraries: Challenging the Current Preclinical Pipeline to Keep the Pace with the Increasing mAb Demand

Zambrano

Froechlich

Lazarevic

et al. 2022

Cancers

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Monoclonal antibodies are among the most powerful therapeutics in modern medicine. Since the approval of the first therapeutic antibody in 1986, monoclonal antibodies keep holding great expectations for application in a range of clinical indications, highlighting the need to provide timely and sustainable access to powerful screening options. However, their application in the past has been limited by time-consuming and expensive steps of discovery and production. The screening of antibody repertoires is a laborious step; however, the implementation of next-generation sequencing-guided screening of single-chain antibody fragments has now largely overcome this issue. This review provides a detailed overview of the current strategies for the identification of monoclonal antibodies from phage display-based libraries. We also discuss the challenges and the possible solutions to improve the limiting selection and screening steps, in order to keep pace with the increasing demand for monoclonal antibodies.

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Section: Discussionmentioning

confidence: 99%

Section: Implementation Of Next Generation Sequencing To Phage Displa...mentioning

confidence: 99%

High-Throughput Monoclonal Antibody Discovery from Phage Libraries: Challenging the Current Preclinical Pipeline to Keep the Pace with the Increasing mAb Demand

Zambrano

Froechlich

Lazarevic

et al. 2022

Cancers

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show abstract

“…Nanopore sequencing has much longer reads, whereas its accuracy is not high enough. Hybrid sequencing by combining different technologies may provide a more comprehensive view of the genome ( Gavrielatos et al, 2021 ; Lin et al, 2021 ). In the current study, Nanopore and Illumina sequencing technologies were used to analyze the genome of Me.…”

Section: Discussionmentioning

confidence: 99%

Hybrid Sequencing Resolved Inverted Terminal Repeats in the Genome of Megavirus Baoshan

2022

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Mimivirus is a group of amoeba-infecting DNA viruses with linear double-strand genome. It is found to be ubiquitous in nature worldwide. Here, we reported the complete genome of a new member of Mimivirus lineage C isolated from a fresh water pond in Shanghai, China. Its 1,224,839-bp genome encoded 1,062 predicted ORFs. Combining the results of Nanopore, Illumina, and Sanger sequencing technologies, two identical 23,919 bp inverted terminal repeats (ITRs) were identified at both extremities of the viral linear genome, one of which was missing in the draft assembly based on Illumina data only. The discovery of ITRs of Mimivirus provided a new insight into Mimivirus genome structure.

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“…The constant development of tools aimed at improving the outcomes of each step will ultimately result in improved assemblies but determining the optimal tools and pipelines to process any particular long read dataset can be a major challenge (Amarasinghe et al 2020). While publications of tool comparisons or benchmarking analyses associated with long-read assembly are not uncommon all benchmarking analyses face tradeoffs that limit how comprehensive they are and thus the scope of their utility (Zhang et al 2020; Cherukuri and Janga 2016; Dohm et al 2020; Gavrielatos et al 2021; Chen et al 2020a; Sun et al 2021; Wick and Holt 2019). For instance, many assessements of program performance focus on few input data sets that may represent a wide range of genetic variation (i.e.…”

Section: Main Textmentioning

confidence: 99%

Harnessing the power of technical and natural variation in 116 yeast datasets to benchmark long read assembly pipelines

Gettle

Gallone

Verstrepen

et al. 2022

Preprint

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With increases in throughput and reductions in cost, long read sequencing has become the standard most genome assembly projects and has opened up new avenues for large-scale genomic research. While more amenable to assembly than short-read sequence data, long-read datasets tend to have higher error rates. To address this problem numerous tools have been developed to correct reads before assembly and polish assembled contigs. Although, numerous studies have been conducted to assess or benchmark these tools, few capture the real variance in long read sequence data that might affect tool performance much less full pipeline performance. To address these shortcomings, we compiled a dataset containing long-read sequences of 116 different strains of brewers yeast, S. cerevisiae, gathered largely from public databases and evaluated different assembly-related tools as well as their interactions. We found that pre-assembly short-read error correction of long reads combined with post-assembly short-read polishing provided the best assemblies. We also found that correction/polishing steps with uncorrected long reads often lead to degradation of assembly quality. Finally, we show which tools and pipelines work best with different types of input data.

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Benchmarking of next and third generation sequencing technologies and their associated algorithms for de novo genome assembly

Cited by 23 publications

References 56 publications

High-Throughput Monoclonal Antibody Discovery from Phage Libraries: Challenging the Current Preclinical Pipeline to Keep the Pace with the Increasing mAb Demand

High-Throughput Monoclonal Antibody Discovery from Phage Libraries: Challenging the Current Preclinical Pipeline to Keep the Pace with the Increasing mAb Demand

Hybrid Sequencing Resolved Inverted Terminal Repeats in the Genome of Megavirus Baoshan

Harnessing the power of technical and natural variation in 116 yeast datasets to benchmark long read assembly pipelines

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