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

Noah Gettle, Brigida Gallone, Kevin Verstrepen, Rike Stelkens
2022 bioRxiv   pre-print
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

Sergey Koren, Michael C Schatz, Brian P Walenz, Jeffrey Martin, Jason T Howard, Ganeshkumar Ganapathy, Zhong Wang, David A Rasko, W Richard McCombie, Erich D Jarvis, Adam M Phillippy
2012 Nature Biotechnology  
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]

Pınar Kavak, Bekir Ergüner, Duran Üstek, Bayram Yüksel, Mahmut Şamil Sağıroğlu, Tunga Güngör, Can Alkan
2016 Lecture Notes in Computer Science  
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

Muhammad Tahir, Muhammad Sardaraz, Ataul Ikram, Hassan Bajwa
2015 Current Bioinformatics  
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

Rei Kajitani, Dai Yoshimura, Yoshitoshi Ogura, Yasuhiro Gotoh, Tetsuya Hayashi, Takehiko Itoh
2020 DNA Research  
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]

Antoine Limasset, Jean-Francois Flot, Pierre Peterlongo
2018 arXiv   pre-print
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

Giles Miclotte, Mahdi Heydari, Piet Demeester, Stephane Rombauts, Yves Van de Peer, Pieter Audenaert, Jan Fostier
2016 Algorithms for Molecular Biology  
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

Ruifeng Hu, Guibo Sun, Xiaobo Sun
2016 BMC Bioinformatics  
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

Niina Haiminen, David N. Kuhn, Laxmi Parida, Isidore Rigoutsos, Andrey Rzhetsky
2011 PLoS ONE  
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?

M. J. Chaisson, D. Brinza, P. A. Pevzner
2008 Genome Research  
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

Jörg A. Bachmann, Andrew Tedder, Benjamin Laenen, Kim A. Steige, Tanja Slotte
2018 G3: Genes, Genomes, Genetics  
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]

Olivia Choudhury, Ankush Chakrabarty, Scott Emrich
2017 bioRxiv   pre-print
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  
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]

Antoine Limasset, Jean-Francois Flot, Pierre Peterlongo
2019 bioRxiv   pre-print
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

M. J. Chaisson, P. A. Pevzner
2008 Genome Research  
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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