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Detection and correction of false segmental duplications caused by genome mis-assembly

David R Kelley, Steven L Salzberg
2010 Genome Biology  
For each genome, we corrected mis-assemblies, improved estimates of the amount of duplicated sequence, and recovered polymorphisms between the sequenced chromosomes.  ...  Identifying false duplications A method for determining false segmental duplications in vertebrate genomes, thus cor-recting mis-assemblies and providing more accurate estimates of duplications.  ...  This work was supported in part by the National Institutes of Health under grants R01-LM006845 to SLS.  ... 
doi:10.1186/gb-2010-11-3-r28 pmid:20219098 pmcid:PMC2864568 fatcat:5mni3znlzbe7zinbg6kyuuxvaq

Hawkeye: an interactive visual analytics tool for genome assemblies

Michael C Schatz, Adam M Phillippy, Ben Shneiderman, Steven L Salzberg
2007 Genome Biology  
Hawkeye is our new visual analytics tool for genome assemblies, designed to aid in identifying and correcting assembly errors.  ...  Users can analyze all levels of an assembly along with summary statistics and assembly metrics, and are guided by a ranking component towards likely mis-assemblies.  ...  This work was supported in part by NIH award R01-LM06845, the National  ... 
doi:10.1186/gb-2007-8-3-r34 pmid:17349036 pmcid:PMC1868940 fatcat:2e7xnrghsrffzcxfirqhdzm4au

Integrating Hi-C links with assembly graphs for chromosome-scale assembly

Jay Ghurye, Arang Rhie, Brian P. Walenz, Anthony Schmitt, Siddarth Selvaraj, Mihai Pop, Adam M. Phillippy, Sergey Koren, Ilya Ioshikhes
2019 PLoS Computational Biology  
Long-read sequencing and novel long-range assays have revolutionized de novo genome assembly by automating the reconstruction of reference-quality genomes.  ...  We demonstrate higher accuracy than the state-of-the-art methods across a variety of Hi-C library preparations and input assembly sizes.  ...  We observed that the 3D-DNA mis-assembly detection was overly aggressive in some cases, and so we ran some assemblies both with and without this feature.  ... 
doi:10.1371/journal.pcbi.1007273 pmid:31433799 pmcid:PMC6719893 fatcat:wmyqazj4cfap3eu4u4ousj653q

GALA: gap-free chromosome-scale assembly with long reads [article]

Mohamed Awad, Xiangchao Gan
2020 bioRxiv   pre-print
Here we propose a chromosome-by-chromosome assembly strategy implemented through the multiple-layer computer graph which identifies mis-assemblies within preliminary assemblies or chimeric raw reads and  ...  High-quality genome assembly has wide applications in genetics and medical studies.  ...  Tsiantis and R. Mott for their helpful comments on the work and Yuxia He for technical support. We also wish to acknowledge S. Morishita for sharing the original C. elegans Pacbio data with us.  ... 
doi:10.1101/2020.05.15.097428 fatcat:ir6pdefcjndylakssjmjdd3t5q

Identifying wrong assemblies in de novo short read primary sequence assembly contigs

Vandna Chawla, Rajnish Kumar, Ravi Shankar
2016 Journal of Biosciences  
[Chawla V, Kumar R and Shankar R 2016 Identifying wrong assemblies in de novo short read primary sequence assembly contigs. J.  ...  Finally, some mis-assembly detecting tools have been evaluated for their ability to detect the wrongly assembled primary contigs, suggesting a lot of scope for improvement in this area.  ...  The proposed mis-assembly detection strategy presented here depends on the features derived after mapping back of reads to the assembled contigs.  ... 
doi:10.1007/s12038-016-9630-0 pmid:27581937 fatcat:qdto3h2aunch3j7uasm7evpghe

EBARDenovo: highly accurate de novo assembly of RNA-Seq with efficient chimera-detection

Hsueh-Ting Chu, William W. L. Hsiao, Jen-Chih Chen, Tze-Jung Yeh, Mong-Hsun Tsai, Han Lin, Yen-Wenn Liu, Sheng-An Lee, Chaur-Chin Chen, Theresa T. H. Tsao, Cheng-Yan Kao
2013 Computer applications in the biosciences : CABIOS  
This algorithm uses an efficient chimera-detection function to abrogate the effect of aberrant chimeric reads in RNA-Seq data.  ...  In a series of assembly experiments, our algorithm is the most accurate among the examined programs, including de Bruijn graph assemblers, Trinity and Oases.  ...  By using 'foreseeable reads' to confirm correct assembly, reads with as small as 15 bp overlaps can be constructed into reliable contigs.  ... 
doi:10.1093/bioinformatics/btt092 pmid:23457040 fatcat:6cnu5tvwx5aptc6omwwefyuwhu

Efficient iterative Hi-C scaffolder based on N-best neighbors

Dengfeng Guan, Shane A. McCarthy, Zemin Ning, Guohua Wang, Yadong Wang, Richard Durbin
2021 BMC Bioinformatics  
Background Efficient and effective genome scaffolding tools are still in high demand for generating reference-quality assemblies.  ...  of contigs.  ...  Availability and requirements Project name: pin_hic. Project home page: https:// github. com/ dfguan/ pin_ hic. Operating system(s): Linux, MacOS. Programming language: C. Other requirements: gcc.  ... 
doi:10.1186/s12859-021-04453-5 pmid:34837944 pmcid:PMC8627104 fatcat:hqiv2xzbqzhaviyrmwus6rypoe

PERGA: A Paired-End Read Guided De Novo Assembler for Extending Contigs Using SVM and Look Ahead Approach

Xiao Zhu, Henry C. M. Leung, Francis Y. L. Chin, Siu Ming Yiu, Guangri Quan, Bo Liu, Yadong Wang, Yan Zhang
2014 PLoS ONE  
We present PERGA (Paired-End Reads Guided Assembler), a novel sequence-reads-guided de novo assembly approach, which adopts greedy-like prediction strategy for assembling reads to contigs and scaffolds  ...  When the correct extension cannot be determined, PERGA will try to extend the contig by all feasible extensions and determine the correct extension by using look-ahead approach.  ...  Acknowledgments The authors thank Qinghua Jiang and Yongdong Xu at Harbin Institute of Technology for informative suggestions. We also thank the reviewers for their constructive comments.  ... 
doi:10.1371/journal.pone.0114253 pmid:25461763 pmcid:PMC4252104 fatcat:taniin2dtvfyfooleugpwjqjia

A novel high-accuracy genome assembly method utilizing a high-throughput workflow [article]

Qingdong Zeng, Wenjin Cao, Liping Xing, Guowei Qin, Jianhui Wu, Michael F. Nagle, Qin Xiong, Jinhui Chen, Liming Yang, Prasad Bajaj, Annapurna Chitikineni, Yan Zhou (+32 others)
2020 biorxiv/medrxiv   pre-print
We also identified 48 large mis-assemblies in the reference wheat genome assembly (IWGSC RefSeq v1.0) and corrected these large mis-assemblies in addition to filling 92.2% of the gaps in RefSeq v1.0.  ...  However, the construction of genome assemblies for various species is often hampered by complexities of genome organization, especially repetitive and complex sequences, leading to mis-assembly and missing  ...  In contrast, for assemblies based on long reads alone or utilizing hybrid sequencing with both long and short reads, mis-assembly is more likely to result from errors or losses in overlap detection due  ... 
doi:10.1101/2020.11.26.400507 fatcat:orru24fxfjgifcwzhicof2cqhe

How well can we create phased, diploid, human genomes?: An assessment of FALCON-Unzip phasing using a human trio [article]

Arkarachai Fungtammasan, Brett Hannigan
2018 bioRxiv   pre-print
Mis-joined boundaries in those contigs are located in areas of low SNP density.  ...  Most mis-phased SNPs are random but present in high frequency toward the end of haplotype contigs.  ...  ACKNOWLEDGEMENTS We would like to thank Nicholas Hill, Eric Talevich, and Samantha Zarate for their comments on the manuscript. This project is fully supported by DNAnexus for computing and storage.  ... 
doi:10.1101/262196 fatcat:anr4npjz6zapxclr2cvd55443q

Iterative error correction of long sequencing reads maximizes accuracy and improves contig assembly

Katrin Sameith, Juliana G. Roscito, Michael Hiller
2016 Briefings in Bioinformatics  
A first step in genome assembly is to computationally correct sequencing errors. However, correcting all errors in these longer reads is challenging.  ...  By combining the advantages of small and large k-mers, this approach corrects more errors in repeats and minimizes the total amount of erroneous reads.  ...  We also thank the members of the Hiller lab and Holger Brandl for helpful comments on the manuscript and the Computer Service Facilities of the MPI-CBG and MPI-PKS for their support.  ... 
doi:10.1093/bib/bbw003 pmid:26868358 pmcid:PMC5221426 fatcat:dbzyh5iodzdjtn23vzavlc6iue

PERGA

Xiao Zhu, Henry C.M. Leung, Francis Y.L. Chin, Siu Ming Yiu, Guangri Quan, Bo Liu, Yadong Wang
2007 Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics - BCB'13  
We present PERGA (Paired-End Reads Guided Assembler), a novel sequence-reads-guided de novo assembly approach, which adopts greedy-like prediction strategy for assembling reads to contigs and scaffolds  ...  We evaluated PERGA on both simulated Illumina data sets and real data sets, and it constructed longer and more correct contigs and scaffolds than other state-of-the-art assemblers IDBA-UD, Velvet, ABySS  ...  ABySS and Velvet both had >200kbp mis-assembled contigs and >300kbp mis-assembled scaffolds, thus their contig coverage dropped dramatically from 96% to 86%, and SGA generated accurate contigs and scaffolds  ... 
doi:10.1145/2506583.2506612 dblp:conf/bcb/ZhuLCYQLW13 fatcat:grbc37yb7bas5h4wzgvsuw63xe

The SAMBA tool uses long reads to improve the contiguity of genome assemblies

Aleksey V. Zimin, Steven L. Salzberg, Mingfu Shao
2022 PLoS Computational Biology  
One strategy to upgrade existing assemblies is to generate additional coverage using long-read data, and add that to the previously assembled contigs.  ...  SAMBA is the only tool of its kind that also computes and fills in the sequence for all spanned gaps in the scaffolds, yielding much longer contigs.  ...  Below we discuss further the issue of detecting contig mis-assemblies. We evaluated how the quality of consensus of the scaffolded assembly varied with the coverage by the additional long read data.  ... 
doi:10.1371/journal.pcbi.1009860 pmid:35120119 pmcid:PMC8849508 fatcat:7g7tigzi55fari26i2j3ctfmu4

Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes

Nathan D. Olson, Todd J. Treangen, Christopher M. Hill, Victoria Cepeda-Espinoza, Jay Ghurye, Sergey Koren, Mihai Pop
2017 Briefings in Bioinformatics  
We also discuss the potential for impact of long-read technologies in metagenomics.  ...  Multiple metagenomic assembly strategies, pipelines and assemblers have appeared in recent years.  ...  Acknowledgements Opinions expressed in this article are of the authors' and do not necessarily reflect the policies and views of NIST or affiliated venues.  ... 
doi:10.1093/bib/bbx098 pmid:28968737 fatcat:gd5iiolxgfdv7f243ngojkyvym

Genome assembly forensics: finding the elusive mis-assembly

Adam M Phillippy, Michael C Schatz, Mihai Pop
2008 Genome Biology  
This work formalizes several mechanisms for detecting mis-assemblies, and describes their implementation in our automated validation pipeline, called amosvalidate.  ...  We demonstrate the application of our pipeline in both bacterial and eukaryotic genome assemblies, and highlight several assembly errors in both draft and finished genomes.  ...  Evaluation of the pipeline has shown it to be highly sensitive for mis-assembly detection, and has revealed mis-assemblies in both draft and finished genomes.  ... 
doi:10.1186/gb-2008-9-3-r55 pmid:18341692 pmcid:PMC2397507 fatcat:xnbbtglp65hfbka4aqvnixpzru
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