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Comparing Assemblies Using Fragments and Mate-Pairs [chapter]

Daniel H. Huson, Aaron L. Halpern, Zhongwu Lai, Eugene W. Myers, Knut Reinert, Granger G. Sutton
2001 Lecture Notes in Computer Science  
The positioning of the fragments (and mate-pairs, if available) in an assembled sequence can be used to evaluate the quality of the assembly and also to compare two different assemblies of the same chromosome  ...  Using current technology, large consecutive stretches of DNA (such as whole chromosomes) are usually assembled from short fragments obtained by shotgun sequencing, or from fragments and mate-pairs, if  ...  given fragment and mate-pair data; see Figure 9 .  ... 
doi:10.1007/3-540-44696-6_23 fatcat:jld7yd3zwfa4dpwiaeyxslosru

Illumina mate-paired DNA sequencing-library preparation using Cre-Lox recombination

Filip Van Nieuwerburgh, Ryan C. Thompson, Jessica Ledesma, Dieter Deforce, Terry Gaasterland, Phillip Ordoukhanian, Steven R. Head
2011 Nucleic Acids Research  
Sequencing reads that pass through the junction of the two joined ends of a 3-5-kb DNA fragment are not easy to identify and pose problems during mapping and de novo assembly.  ...  Standard Illumina mate-paired libraries are constructed from 3-to 5-kb DNA fragments by a blunt-end circularization.  ...  We compared assembly performance using only the LoxP-positive paired-end reads to assembly performance using the same data complemented with a scaffolding step using the LoxP-positive mate-paired and the  ... 
doi:10.1093/nar/gkr1000 pmid:22127871 pmcid:PMC3273786 fatcat:iscv6i2h7rgl3f35hvtpp7fuxm

Generation of Long Insert Pairs Using a Cre-LoxP Inverse PCR Approach

Ze Peng, Zhiying Zhao, Nandita Nath, Jeff L. Froula, Alicia Clum, Tao Zhang, Jan-fang Cheng, Alex C. Copeland, Len A. Pennacchio, Feng Chen, Matteo Pellegrini
2012 PLoS ONE  
Large insert mate pair reads have a major impact on the overall success of de novo assembly and the discovery of inherited and acquired structural variants.  ...  The positional information of mate pair reads generally improves genome assembly by resolving repeat elements and/or ordering contigs.  ...  Overall, results are comparable between contigs assembled using CLIP-PE or the simulated mate-pair reads, suggesting that CLIP-PE library quality is very high.  ... 
doi:10.1371/journal.pone.0029437 pmid:22253722 pmcid:PMC3253782 fatcat:jigizennl5gmlgltriuuwshl54

Fournierella massiliensis gen. nov., sp. nov., a new human-associated member of the family Ruminococcaceae

2017 International Journal of Systematic and Evolutionary Microbiology  
To demonstrate the use of mate pair libraries for de novo assembly, the genome of E. coli K-12 MG1655-a laboratory strain of bacteria used to benchmark many NGS applications-was assembled.  ...  As such, aligned mate pair datasets can inform on genomic regions separated by larger distances compared to traditional paired-end datasets.  ... 
doi:10.1099/ijsem.0.001826 pmid:28126042 fatcat:di3d3kfkfzf2bnmwg2vbrht3xi

Design of a compartmentalized shotgun assembler for the human genome

D. H. Huson, K. Reinert, S. A. Kravitz, K. A. Remington, A. L. Delcher, I. M. Dew, M. Flanigan, A. L. Halpern, Z. Lai, C. M. Mobarry, G. G. Sutton, E. W. Myers
2001 Bioinformatics  
An interim strategy employed at Celera, called compartmentalized shotgun assembly, makes use of preliminary data produced by both approaches.  ...  In this paper we describe the design, implementation and operation of the "compartmentalized shotgun assembler".  ...  We would like to thank our colleagues Mike Flanigan, Randall Bolaños, and Laurent Mouchard.  ... 
doi:10.1093/bioinformatics/17.suppl_1.s132 pmid:11473002 fatcat:6sfgejup7zcwbdaksf2njpdpye

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  ...  assembly). 5 Table 1 and Figure 6 compare EULER-USR and Velvet and illustrate that mate-pairs significantly improve the assemblies.  ... 
doi:10.1101/gr.079053.108 pmid:19056694 pmcid:PMC2652199 fatcat:5447bmmkkvdhrkkbqxudrsifc4

Fragment assembly with double-barreled data

P. A. Pevzner, H. Tang
2001 Bioinformatics  
For the last twenty years fragment assembly was dominated by the "overlap -layout -consensus" algorithms that are used in all currently available assembly tools.  ...  For long nearly-perfect repeats this question is notoriously difficult and some copies of such repeats may be "lost" in genomic assemblies.  ...  We are grateful to Michael Fonstein, Eugene Goltsman, Zufar Mulyukov, Julian Parkhill, Alexei Sorokine, and Michael Waterman for useful discussions and providing sequencing data.  ... 
doi:10.1093/bioinformatics/17.suppl_1.s225 pmid:11473013 fatcat:r7vcy6yhffbezowzs6rexndy6e

Whole-genome sequencing of Nicotiana glauca [article]

Galina Khafizova, Pavel Dobrynin, Dmitrii Polev, Tatyana Matveeva
2017 bioRxiv   pre-print
These genome data could be used in pharmacological and in phylogenetic studies.  ...  Conclusion: We provide the first comprehensive de novo full genome assembly of three tobacco, and a cT-DNA insertion analysis.  ...  Acknowledgements The authors thank Professor Otten (Institut de Biologie Moléculaire des Plantes, Strasbourg) and Professor Lutova (Saint Petersburg University, St.Petersburg) for useful discussion and  ... 
doi:10.1101/211482 fatcat:p3tuojpc7zdvdkgnqbzixyvlti

NeatFreq: reference-free data reduction and coverage normalization for De Novosequence assembly

Jamison M McCorrison, Pratap Venepally, Indresh Singh, Derrick E Fouts, Roger S Lasken, Barbara A Methé
2014 BMC Bioinformatics  
The results obtained from conventional Overlap-Layout-Consensus (OLC) were compared to simulated multi-de Bruijn graph assembly alternatives trained for variable coverage input using sequence before and  ...  Coverage reduction was shown to increase processing speed and reduce memory requirements when using conventional bacterial assembly algorithms.  ...  to maintain fragment and mate pair relationships (Optional) Parse 2-sided mates from fragment-only runs using read IDs Random selection The number of reads selected from each bin is determined by the  ... 
doi:10.1186/s12859-014-0357-3 pmid:25407910 pmcid:PMC4245761 fatcat:htncoivbn5gxlnfliuj53unsjm

Genomic and transcriptomic data production for helminths

Rahul Tyagi, John Martin, Makedonka Mitreva
2018 Protocol Exchange  
Protocols for genomic and transcriptomic data production, assembly and quality control.  ...  For 454 sequencing, FLX Titanium paired-end library adaptors are ligated onto the immobilized performed to isolate 300-500 bp library fragments. 454/Illumina 8 kb insert mate pair libraries 8kb mate  ...  DNA is sheared into 3kb fragments, blunt ended and ligated to the SOLiD Mate-Pair Cap Adapter (ABI). 2. Ligated DNA is size fractionated to 2-4 kb fractions and then purified. 3.  ... 
doi:10.1038/protex.2018.044 fatcat:w7wsdxb6sveghp4nhofmpw22ni

Simplifier: a web tool to eliminate redundant NGS contigs

Rommel Thiago Jucá Ramos, Adriana Ribeiro Carneiro, Vasco Azevedo, Maria Paula Schneider, Debmalya Barh, Artur Silva
2012 Bioinformation  
Processing the contigs of Escherichia coli DH10B with Simplifier reduced the mate-paired library 17.47% and the fragment library 23.91%.  ...  Additionally after abinitio assembly, curation of the hundreds or thousands of contigs generated by assemblers demands considerable time and computational resources.  ...  M.P.S, A.S., V.A. and A.R.C. were supported by Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq).  ... 
doi:10.6026/97320630008996 pmid:23275695 pmcid:PMC3524941 fatcat:vwfx3cfn6rhrbkozm5tnvbdypq

Genome assembly reborn: recent computational challenges

M. Pop
2009 Briefings in Bioinformatics  
In this article, we outline the major algorithmic approaches for genome assembly and describe recent developments in this domain.  ...  In addition, the low cost of next generation sequencing data has led to an increased use of sequencing in new settings.  ...  read pairs (mate-pairs) that are separated by a known distance (the size of the original fragment).  ... 
doi:10.1093/bib/bbp026 pmid:19482960 pmcid:PMC2691937 fatcat:g2azb2q5ing3lej52jny2xiohq

Long-span, mate-pair scaffolding and other methods for faster next-generation sequencing library creation

Cheng-Cang Wu, Rosa Ye, Svetlana Jasinovica, Megan Wagner, Ronald Godiska, Amy Hin-Yan Tong, Si Lok, Amanda Krerowicz, Curtis Knox, David Mead, Michael Lodes
2012 Nature Methods  
The NxSeq™ 40 kb Mate-Pair Cloning Kit has been developed to facilitate genome assembly and gap closure.  ...  Large insert mate-pair reads have a major impact on the overall success of de novo genome assembly and the discovery of inherited and acquired structural variants.  ...  to create long-span, mate-pair libraries for de novo genome assembly.  ... 
doi:10.1038/nmeth.f.358 fatcat:bj3r3nx7are4vjo77f2hvgatiq

A hierarchical network heuristic for solving the orientation problem in genome assembly [article]

Karl R. B. Schmitt, Aleksey V. Zimin, Guillaume Marcaçs, James A. Yorke, Michelle Girvan
2013 arXiv   pre-print
A mate pair is a set of two reads that are sequenced from the ends of a single fragment of DNA, and therefore have opposite mutual orientations.  ...  This process involves building ordered and oriented linear collections of contigs (continuous overlapping sequence reads) called scaffolds and relies on the use of mate pair data.  ...  of Food and Agriculture.  ... 
arXiv:1307.0541v1 fatcat:6wfje2enhbg5fg5biliet22yrm

Whole genome sequence and de novo assembly revealed genomic architecture of Indian Mithun (Bos frontalis) [chapter]

Sabyasachi Mukherjee, Zexi Cai, Anupama Mukherjee, Imsusosang Longkumer, Moonmoon Mech, Kezhavituo Vupru, Kobu Khate, Chandan Rajkhowa, Bernt Guldbrandtsen, Mogens Sandø Lund, Goutam Sahana
2020 Prime Archives in Genetics  
Genomic Data Processing, Genome Assemble and Assembly Assessment Trimmomatic [54] was used to remove the adaptor and trim the raw data of Illumina paired-end (PE) sequencing and mate-pair (MP) sequencing  ...  alignment of pair-end (PE) library, 3 Kb mate-pair (MP) library and 5 Kb MP library to assembly.  ... 
doi:10.37247/pag.1.2020.13 fatcat:ot2mov3q3rdq3cqdsymzoi7bnm
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