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Harnessing the power of technical and natural variation in 116 yeast datasets to benchmark long read assembly pipelines
[article]
2022
bioRxiv
pre-print
Preserved Fulltext
While more amenable to assembly than short-read sequence data, long-read datasets tend to have higher error rates. ...
We found that pre-assembly short-read error correction of long reads combined with post-assembly short-read polishing provided the best assemblies. ...
Palmer and the members of the Stelkens lab for statistical and conceptual advice.
Funding: Swedish Research Council 2017-04963 (RS) Knut and Alice Wallenberg Foundation 2017.0163 (RS) ...
doi:10.1101/2022.03.17.484703
fatcat:iuvuf6bdxjdyji3j2ycvliddae
Hybrid error correction and de novo assembly of single-molecule sequencing reads
2012
Nature Biotechnology
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However, the error rates of single-molecule reads are high, which has limited their use thus far to resequencing bacteria. ...
To address this limitation, we introduce a correction algorithm and assembly strategy that uses short, highfidelity sequences to correct the error in single-molecule sequences. ...
Consistent with the results reported above for genome assembly, the corrected RNA-Seq sequences had very low error rates, with only 0.06% insertion and 0.02% deletion rates. ...
doi:10.1038/nbt.2280
pmid:22750884
pmcid:PMC3707490
fatcat:wiou4fgizjdobow5mbedgzyqm4
Improving Genome Assemblies Using Multi-platform Sequence Data
[chapter]
2016
Lecture Notes in Computer Science
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De novo assembly using short reads generated by next generation sequencing technologies is still an open problem. ...
There is still a need for computational approaches to improve draft assemblies. ...
In addition, the data quality is in fact lower, with greater error rates, and short read lengths for most platforms. ...
doi:10.1007/978-3-319-44332-4_17
fatcat:elq5f4esmjasdfhsslmkiskavq
HaShRECA: Hadoop Based Short Read Error Correction Algorithm for Genome Assembly
2015
Current Bioinformatics
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The NGS technologies generate short sequences that are prone to high error rates [31] [32] . So, assemblies of long repeats and duplication suffer fro m short read length [33] . ...
In this paper, we present review of and measuring parameters associated with genome sequence short read errors correction tools and algorithms. ...
It is used to correct sequencing errors in high throughput short read data for Roche/454 platform. It is based on spectral align ment method. ...
doi:10.2174/157489361004150922151409
fatcat:vwgh4v3rdbdjnjlueis5roqznq
Platanus_B: an accurate de novo assembler for bacterial genomes using an iterative error-removal process
2020
DNA Research
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Although the hybrid strategies for short and long reads were effective in achieving near full-length genomes, we found that short read-only assemblies generated with Platanus_B were sufficient to obtain ...
De novo assembly of short DNA reads remains an essential technology, especially for large-scale projects and high-resolution variant analyses in epidemiology. ...
also applied, but combined with short reads to improve the accuracy of the assembled sequences in certain studies. 22 In other words, the short-read genomic sequencing is still a practical method in ...
doi:10.1093/dnares/dsaa014
pmid:32658266
pmcid:PMC7433917
fatcat:arb2g5babneofbahqblogvmpia
Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs
[article]
2018
arXiv
pre-print
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Motivations Short-read accuracy is important for downstream analyses such as genome assembly and hybrid long-read correction. ...
Results We propose a new method to correct short reads using de Bruijn graphs, and implement it as a tool called Bcool. As a first st ep, Bcool constructs a compacted de Bruijn graph from the reads. ...
Applying LoRDEC using non-corrected short reads lead to a 3.04% error rate on corrected long reads. ...
arXiv:1711.03336v2
fatcat:mdsod7nqsbfmdicgly7lgvudnq
Jabba: hybrid error correction for long sequencing reads
2016
Algorithms for Molecular Biology
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While the improved read length can provide useful information for downstream analysis, underlying algorithms are challenged by the high error rate. ...
Third generation sequencing platforms produce longer reads with higher error rates than second generation technologies. ...
Every sequencing technology results in reads that contain errors, with error profiles varying greatly between platforms. ...
doi:10.1186/s13015-016-0075-7
pmid:27148393
pmcid:PMC4855726
fatcat:c7wxdtplrrgjtc6k4lxbyfcahu
LSCplus: a fast solution for improving long read accuracy by short read alignment
2016
BMC Bioinformatics
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However, the raw data from SMRT sequencing are of relatively low quality, with a random error rate of approximately 15 %, for which error correction using next-generation sequencing (NGS) short reads is ...
Results: Here, we report an improved tool (LSCplus) for error correction with the LSC program as a reference. LSCplus overcomes the disadvantage of LSC's time consumption and improves quality. ...
We thank the developers for their contributions to LSC, which we have referenced, and we thank the IMPLAD webserver managers for providing the servers to code and test our programs. ...
doi:10.1186/s12859-016-1316-y
pmid:27829364
pmcid:PMC5103424
fatcat:5eciwrfjrzdonmh6r2ivgxtevq
Evaluation of Methods for De Novo Genome Assembly from High-Throughput Sequencing Reads Reveals Dependencies That Affect the Quality of the Results
2011
PLoS ONE
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and the observed sequencing error rates are powerful variables that affect the best achievable assembly of the target sequence in terms of size and correctness. ...
Recent developments in high-throughput sequencing technology have made low-cost sequencing an attractive approach for many genome analysis tasks. ...
Acknowledgments We would like to thank the Cacao Genome Sequencing Consortium (http://www.cacaogenomedb.org/) for motivating discussions, Tien Huynh for setting up the assembly programs and reference sequences ...
doi:10.1371/journal.pone.0024182
pmid:21915294
pmcid:PMC3168497
fatcat:mslrdxt44vgmrda4fwpfy3hawa
De novo fragment assembly with short mate-paired reads: Does the read length matter?
2008
Genome Research
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We are grateful to Ronan O'Malley and Joseph Ecker for providing us with the BAC reads. ...
We thank Dirk Evers, Klaus Maisinger, and Jacques Retief for insightful discussions about the Illumina technology and to Xiaohua Huang and Eric Roller for many discussions on emerging next-generation sequencing ...
No existing short read assembly tool can efficiently deal with such high error rates and the conventional wisdom is that the read tails become unusable when the error rate exceeds 3%. ...
doi:10.1101/gr.079053.108
pmid:19056694
pmcid:PMC2652199
fatcat:5447bmmkkvdhrkkbqxudrsifc4
Targeted Long-Read Sequencing of a Locus Under Long-Term Balancing Selection in Capsella
2018
G3: Genes, Genomes, Genetics
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We further find that short-read sequencing is a valuable complement, allowing correction of the relatively high rate of indel errors that result from this approach. ...
A similar error rate was estimated based on comparison of Illumina short-read sequences and BAC assemblies. ...
Current high throughput sequencing technologies show between 0.1 and $12% error rate of raw reads, with Illumina short read technologies generally below 1% and SMRT sequencing .10%, reviewed in (Reuter ...
doi:10.1534/g3.117.300467
pmid:29476024
pmcid:PMC5873921
fatcat:zy5a2v7g5rdqlk27fnwv3na4ia
HECIL: A Hybrid Error Correction Algorithm for Long Reads with Iterative Learning
[article]
2017
bioRxiv
pre-print
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Currently, the usefulness of such long reads is limited, however, because of high sequencing error rates. ...
Second-generation sequencing techniques generate short reads that can result in fragmented genome assemblies. ...
Acknowledgements This work was supported by the Eck Institute for Global Health (EIGH) Ph.D. fellowship to Choudhury, and NIH R21AI123967 to Emrich. ...
doi:10.1101/162917
fatcat:k6arbfcgrrgsre43pslhcs3rga
Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs
2019
Bioinformatics
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Short-read accuracy is important for downstream analyses such as genome assembly and hybrid long-read correction. ...
Despite much work on short-read correction, present-day correctors either do not scale well on large datasets or consider reads as mere suites of k-mers, without taking into account their full-length sequence ...
Applying LoRDEC using non-corrected short reads lead to a 3.04% error rate on corrected long reads. ...
doi:10.1093/bioinformatics/btz102
pmid:30785192
fatcat:bfnvztlenjcchnmmhjcfab7qlq
Toward perfect reads: short reads correction via mapping on compacted de Bruijn graphs
[article]
2019
bioRxiv
pre-print
Preserved Fulltext
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Motivations: Short-read accuracy is important for downstream analyses such as genome assembly and hybrid long-read correction. ...
Results: We propose a new method to correct short reads using de Bruijn graphs, and implement it as a tool called Bcool. As a first step, Bcool constructs a compacted de Bruijn graph from the reads. ...
Applying LoRDEC using non-corrected short reads lead to a 3.04% error rate on corrected long reads. ...
doi:10.1101/558395
fatcat:phdjwwhf3rczrmfoorzxbk33l4
Short read fragment assembly of bacterial genomes
2008
Genome Research
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Huang et al. (2003) and Jaffe et al. (2003) for efficient construction of the repeat graph even in the simple case of SBH "reads." ...
For example, while the study by Pevzner et al. (1989) described a simple algorithm for constructing the SBH repeat graph, it is not immediately clear how to generalize the approaches in the studies by ...
We thank Xiaohua Huang and Eric Roller for many helpful discussions on emerging short read technologies. ...
doi:10.1101/gr.7088808
pmid:18083777
pmcid:PMC2203630
fatcat:drv2xvemkbgchgvbeni3ufhyji
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