Performance difference of graph-based and alignment-based hybrid error correction methods for error-prone long reads

Wang, Anqi; Au, Kin Fai

doi:10.1186/s13059-019-1885-y

Cited by 9 publications

(8 citation statements)

References 34 publications

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“…SGS has the advantages of low cost, high accuracy and short sequencing time, but shorter sequence read lengths; TGS has longer sequence reads but higher error rates [ 47 ]. As a result, more and more studies on the response to plant stress are now beginning to make use of combined SGS and TGS sequencing methods, which can provide a more complete and high-quality assembly at the transcriptome level [ 48 – 50 ].…”

Section: Discussionmentioning

confidence: 99%

Full-length transcriptome sequencing reveals the molecular mechanism of potato seedlings responding to low-temperature

et al. 2022

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Background Potato (Solanum tuberosum L.) is one of the world's most important crops, the cultivated potato is frost-sensitive, and low-temperature severely influences potato production. However, the mechanism by which potato responds to low-temperature stress is unclear. In this research, we apply a combination of second-generation sequencing and third-generation sequencing technologies to sequence full-length transcriptomes in low-temperature-sensitive cultivars to identify the important genes and main pathways related to low-temperature resistance. Results In this study, we obtained 41,016 high-quality transcripts, which included 15,189 putative new transcripts. Amongst them, we identified 11,665 open reading frames, 6085 simple sequence repeats out of the potato dataset. We used public available genomic contigs to analyze the gene features, simple sequence repeat, and alternative splicing event of 24,658 non-redundant transcript sequences, predicted the coding sequence and identified the alternative polyadenylation. We performed cluster analysis, GO, and KEGG functional analysis of 4518 genes that were differentially expressed between the different low-temperature treatments. We examined 36 transcription factor families and identified 542 transcription factors in the differentially expressed genes, and 64 transcription factors were found in the AP2 transcription factor family which was the most. We measured the malondialdehyde, soluble sugar, and proline contents and the expression genes changed associated with low temperature resistance in the low-temperature treated leaves. We also tentatively speculate that StLPIN10369.5 and StCDPK16 may play a central coordinating role in the response of potatoes to low temperature stress. Conclusions Overall, this study provided the first large-scale full-length transcriptome sequencing of potato and will facilitate structure–function genetic and comparative genomics studies of this important crop.

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Section: Discussionmentioning

confidence: 99%

Full-length transcriptome sequencing reveals the molecular mechanism of potato seedlings responding to low-temperature

et al. 2022

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“…A high quality de novo genome assembly using only ONT reads would require high sequencing quality on base accuracy, long read length, and great sequencing depth (Tyson et al, 2018; Vaser et al, 2017), increasing the sequencing cost. By introducing the high accuracy short reads to the assembly polishing, most errors could be corrected as long as the long reads error rate was below 15 % (Wang and Au, 2020), and the requirement on long read coverage can be decreased. The improvement on sequence accuracy provides great advantages to the BUSCO score and gene annotation (Johnson et al, 2020).…”

Section: Discussionmentioning

confidence: 99%

“…Moreover, long reads can span the entire tandems of repeats in the genome, resolve the complex regions and improve contiguity that short reads could not achieved (Shin et al, 2019; Tyson et al, 2018). On the other hand, short read polishing could make up the problem of high error rate in long read assembly and cut down the requirement of sequencing depth (Wang and Au, 2020). Therefore, hybrid assembly method greatly improves the genome assembly quality and cuts down the unit price of data generation (Díaz-Viraqué et al, 2019; Miller et al, 2017; Tan et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Chromosome-levelde novoassembly ofCoprinopsis cinerea A43mut B43mut pab1-1#326 and genetic variant identification of mutants using Nanopore MinION sequencing

Xie

Zhong

Chang

et al. 2020

Preprint

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The homokaryotic Coprinopsis cinerea strain A43mut B43mut pab1-1 #326 is a widely used experimental model for developmental studies in mushroom-forming fungi. It can grow on defined artificial media and complete the whole lifecycle within two weeks. The mutations in mating type factors A and B result in the special feature of clamp formation and fruiting without mating. This feature allows investigations and manipulations with a homokaryotic genetic background. Current genome assembly of strain #326 was based on short-read sequencing data and was highly fragmented, leading to the bias in gene annotation and downstream analyses. Here, we report a chromosome-level genome assembly of strain #326. Oxford Nanopore Technology (ONT) MinION sequencing was used to get long reads. Illumina short reads was used to polish the sequences. A combined assembly yield 13 chromosomes and a mitochondrial genome as individual scaffolds. The assembly has 15,250 annotated genes with a high synteny with the C. cinerea strain Okayama-7 #130. This assembly has great improvement on contiguity and annotations. It is a suitable reference for further genomic studies, especially for the genetic, genomic and transcriptomic analyses in ONT long reads. Single nucleotide variants and structural variants in six mutagenized and cisplatin-screened mutants could be identified and validated. A 66 bp deletion in Ras GTPase-activating protein (RasGAP) was found in all mutants. To make a better use of ONT sequencing platform, we modified a high-molecular-weight genomic DNA isolation protocol based on magnetic beads for filamentous fungi. This study showed the use of MinION to construct a fungal reference genome and to perform downstream studies in an individual laboratory. An experimental workflow was proposed, from DNA isolation and whole genome sequencing, to genome assembly and variant calling. Our results provided solutions and parameters for fungal genomic analysis on MinION sequencing platform.HighlightA chromosome-level genome assembly of C. cinerea #326A fast and efficient high-molecular-weight fungal genomic DNA isolation protocolStructural variant and single nucleotide variant calling using Nanopore readsA series of solutions and reference parameters for fungal genomic analysis on MinION

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“…Previous papers already covered this topic. On the one hand, [24] and [70] focused on hybrid correction. The former proposed a benchmark of ten tools on five datasets, whereas the latter studied performances of graph-based and alignment-based methods.…”

Section: Contributionmentioning

confidence: 99%

Long-read error correction: a survey and qualitative comparison

Morisse

Lecroq

Lefèbvre

2020

Preprint

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Third generation sequencing technologies Pacific Biosciences and Oxford Nanopore Technologies were respectively made available in 2011 and 2014. In contrast with second generation sequencing technologies such as Illumina, these new technologies allow the sequencing of long reads of tens to hundreds of kbps. These so called long reads are particularly promising, and are especially expected to solve various problems such as contig and haplotype assembly or scaffolding, for instance. However, these reads are also much more error prone than second generation reads, and display error rates reaching 10 to 30%, according to the sequencing technology and to the version of the chemistry. Moreover, these errors are mainly composed of insertions and deletions, whereas most errors are substitutions in Illumina reads. As a result, long reads require efficient error correction, and a plethora of error correction tools, directly targeted at these reads, were developed in the past nine years. These methods can adopt a hybrid approach, using complementary short reads to perform correction, or a self-correction approach, only making use of the information contained in the long reads sequences. Both these approaches make use of various strategies such as multiple sequence alignment, de Bruijn graphs, hidden Markov models, or even combine different strategies. In this paper, we describe a complete survey of long-read error correction, reviewing all the different methodologies and tools existing up to date, for both hybrid and self-correction. Moreover, the long reads characteristics, such as sequencing depth, length, error rate, or even sequencing technology, can have an impact on how well a given tool or strategy performs, and can thus drastically reduce the correction quality. We thus also present an in-depth benchmark of available long-read error correction tools, on a wide variety of datasets, composed of both simulated and real data, with various error rates, coverages, and read lengths, ranging from small bacterial to large mammal genomes.2. Alignment of long reads and contigs obtained from short reads assembly. In the same fashion, long reads can also be corrected with the help of the contig they align to, by computing consensus sequences from these contigs. ECTools [43], HALC [6], and MiRCA [30] adopt this methodology. 3. Use of de Bruijn graphs, built from the short reads' k-mers. Once built, the long reads can indeed be anchored to the graph. It can then be traversed, in order to find paths allowing to link together anchored regions of the long reads, and thus correct unanchored regions. LoRDEC [59], Jabba [52], FMLRC [67], and ParLECH [16] rely on this strategy.4. Use of Hidden Markov Models. These can indeed be used in order to represent the long reads. The models can then be trained with the help of short reads, in order to extract consensus sequences, representing the corrected long reads. Hercules [21] is based on this approach.Other methods, such as NaS [49] and HG-CoLoR [53], combine different of the aforementioned ...

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Performance difference of graph-based and alignment-based hybrid error correction methods for error-prone long reads

Cited by 9 publications

References 34 publications

Full-length transcriptome sequencing reveals the molecular mechanism of potato seedlings responding to low-temperature

Full-length transcriptome sequencing reveals the molecular mechanism of potato seedlings responding to low-temperature

Chromosome-levelde novoassembly ofCoprinopsis cinerea A43mut B43mut pab1-1#326 and genetic variant identification of mutants using Nanopore MinION sequencing

Long-read error correction: a survey and qualitative comparison

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