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Next-Generation DNA Sequencing/Review: Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses
- Melissa J. Fullwood,
- Chia-Lin Wei,
- Edison T. Liu,
- and Yijun Ruan
Genome Res. April 2009 19: 521-532; doi:10.1101/gr.074906.107
...constructs can be analyzed by concatemer sequencing using Sanger capillary instrument, dimerization sequencing using Roche 454 GS, paired-end sequencing using Illumina GA or Applied Biosystems SOLiD. The PET sequences are then mapped to reference sequences to demarcate the boundaries of the target DNA...
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Method: Efficient and unique cobarcoding of second-generation sequencing reads from long DNA molecules enabling cost-effective and accurate sequencing, haplotyping, and de novo assembly
- Ou Wang,
- Robert Chin,
- Xiaofang Cheng,
- Michelle Ka Yan Wu,
- Qing Mao,
- Jingbo Tang,
- Yuhui Sun,
- Ellis Anderson,
- Han K. Lam,
- Dan Chen,
- Yujun Zhou,
- Linying Wang,
- Fei Fan,
- Yan Zou,
- Yinlong Xie,
- Rebecca Yu Zhang,
- Snezana Drmanac,
- Darlene Nguyen,
- Chongjun Xu,
- Christian Villarosa,
- Scott Gablenz,
- Nina Barua,
- Staci Nguyen,
- Wenlan Tian,
- Jia Sophie Liu,
- Jingwan Wang,
- Xiao Liu,
- Xiaojuan Qi,
- Ao Chen,
- He Wang,
- Yuliang Dong,
- Wenwei Zhang,
- Andrei Alexeev,
- Huanming Yang,
- Jian Wang,
- Karsten Kristiansen,
- Xun Xu,
- Radoje Drmanac,
- and Brock A. Peters
Genome Res. May 2019 29: 798-808; Published in Advance April 2, 2019, doi:10.1101/gr.245126.118
..., but not shared with the standard library made from GIAB reference material. We also compared cell line DNA FPs with the Chromium library sequenced using Illumina technology and found that 1268 of these shared FPs were also present in the Chromium library (Supplemental Fig. S1B). Examination of the distribution...
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Resource: Single-cell strand sequencing of a macaque genome reveals multiple nested inversions and breakpoint reuse during primate evolution
- Flavia Angela Maria Maggiolini,
- Ashley D. Sanders,
- Colin James Shew,
- Arvis Sulovari,
- Yafei Mao,
- Marta Puig,
- Claudia Rita Catacchio,
- Maria Dellino,
- Donato Palmisano,
- Ludovica Mercuri,
- Miriana Bitonto,
- David Porubský,
- Mario Cáceres,
- Evan E. Eichler,
- Mario Ventura,
- Megan Y. Dennis,
- Jan O. Korbel,
- and Francesca Antonacci
Genome Res. November 2020 30: 1680-1693; Published in Advance October 22, 2020, doi:10.1101/gr.265322.120
..., gorilla, orangutan, and macaque BAC libraries (CHORI-251, CHORI-277, CHORI-276, CHORI-250, and CHORI-259) and fosmid-end sequences of gorilla fosmid library (CHORI-1277) were obtained from the NIH trace repository and mapped against the human reference (GRCh38/hg38) following a protocol optimized...
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Method: Single-pollen-cell sequencing for gamete-based phased diploid genome assembly in plants
- Dongqing Shi,
- Jun Wu,
- Haibao Tang,
- Hao Yin,
- Hongtao Wang,
- Ran Wang,
- Runze Wang,
- Ming Qian,
- Juyou Wu,
- Kaijie Qi,
- Zhihua Xie,
- Zhiwen Wang,
- Xiang Zhao,
- and Shaoling Zhang
Genome Res. November 2019 29: 1889-1899; Published in Advance October 24, 2019, doi:10.1101/gr.251033.119
...-fold depth of reference coverage on the Illumina HiSeq 2000/4000 platform with 100/125 nt double paired ends. After removing adapter sequences as well as ambiguous and/or low-quality reads, a total of 0.98 billion reads covering an average of ∼66% of the pear reference were generated for each single...
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Method: HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
- Peter Edge,
- Vineet Bafna,
- and Vikas Bansal
Genome Res. May 2017 27: 801-812; Published in Advance December 9, 2016, doi:10.1101/gr.213462.116
...Bio) generate long sequence reads (2–20 kb in length) that can directly enable -wide haplotyping. Pendleton and colleagues demonstrated the feasibility of assembling haplotypes from SMRT reads using variants identified from short read Illumina sequencing (Pendleton et al. 2015). Haplotype assembly is also...
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Method: Direct chromosome-length haplotyping by single-cell sequencing
- David Porubský,
- Ashley D. Sanders,
- Niek van Wietmarschen,
- Ester Falconer,
- Mark Hills,
- Diana C.J. Spierings,
- Marianna R. Bevova,
- Victor Guryev,
- and Peter M. Lansdorp
Genome Res. November 2016 26: 1565-1574; Published in Advance September 19, 2016, doi:10.1101/gr.209841.116
...generated using the HiSeq 2500 sequencing platform (Illumina) following the manufacturer’s instructions. For 50-bp- and 100-bp-long reads, 192 and 96 single-cell libraries were pooled together, respectively, and sequenced in one lane of the rapid run flow cell. Each plate included two 10-cell controls...
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Resource: Long-read sequencing reveals intra-species tolerance of substantial structural variations and new subtelomere formation in C. elegans
- Chuna Kim,
- Jun Kim,
- Sunghyun Kim,
- Daniel E. Cook,
- Kathryn S. Evans,
- Erik C. Andersen,
- and Junho Lee
Genome Res. June 2019 29: 1023-1035; Published in Advance May 23, 2019, doi:10.1101/gr.246082.118
...performed flash-freeze/thaw cycles 10×. RNA was extracted using chloroform and isopropanol precipitation. Macrogen performed library preparation and sequencing using HiSeq 4000 (Illumina) with 101-bp paired-end reads. Technical duplicate samples were sequenced in this study.Genome assembly and polishing...
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Method: Reconstructing complex regions of genomes using long-read sequencing technology
- John Huddleston,
- Swati Ranade,
- Maika Malig,
- Francesca Antonacci,
- Mark Chaisson,
- Lawrence Hon,
- Peter H. Sudmant,
- Tina A. Graves,
- Can Alkan,
- Megan Y. Dennis,
- Richard K. Wilson,
- Stephen W. Turner,
- Jonas Korlach,
- and Evan E. Eichler
Genome Res. April 2014 24: 688-696; Published in Advance January 13, 2014, doi:10.1101/gr.168450.113
...by mapping fosmid paired-end sequences to the final assemblies. Clones that failed to assemble into a single contig could be subjected to higher coverage using one clone prep per SMRT Cell. For s without fosmid end sequence data, gel extraction of DNA and sequencing using orthogonal chemistries would...
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Methods: A new strategy for genome assembly using short sequence reads and reduced representation libraries
- Andrew L. Young,
- Hatice Ozel Abaan,
- Daniel Zerbino,
- James C. Mullikin,
- Ewan Birney,
- and Elliott H. Margulies
Genome Res. February 2010 20: 249-256; doi:10.1101/gr.097956.109
.... A subsequent bead purification step eliminated unbound adapter sequences from the preparation. Single-end sequencing reads, 30–48 bases in length, for each of the eight libraries, were sequenced on the Illumina Table 3. The contigs generated with Velvet and Minimus were scaffolded using paired-end genomic...
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Resource: Impact of genomic structural variation in Drosophila melanogaster based on population-scale sequencing
- Thomas Zichner,
- David A. Garfield,
- Tobias Rausch,
- Adrian M. Stütz,
- Enrico Cannavó,
- Martina Braun,
- Eileen E.M. Furlong,
- and Jan O. Korbel
Genome Res. March 2013 23: 568-579; Published in Advance December 6, 2012, doi:10.1101/gr.142646.112
...nucleotide resolution SV map will facilitate further investigations of the interplay of coding and noncoding functional elements in the fruit fly , including cis regulatory elements. Methods DNA sequencing, sequence data retrieval, and read mapping Illumina paired-end sequencing data were obtained from...

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