Results 11 to 20 of about 420,786 (307)

Improved Protocols for Illumina Sequencing [PDF]

Current Protocols in Human Genetics, 2013
AbstractIn this unit, we describe a set of improvements that have been made to the standard Illumina protocols to make the sequencing process more reliable in a high‐throughput environment, reduce amplification bias, narrow the distribution of insert sizes, and reliably obtain high yields of data. Curr. Protoc. Hum. Genet. 79:18.2.1‐18.2.42.
Iraad F, Bronner, Michael A, Quail, Daniel J, Turner, Harold, Swerdlow   +3 more
openaire   +3 more sources

Structural variant analysis of a cancer reference cell line sample using multiple sequencing technologies

Genome Biology, 2022
Background The cancer genome is commonly altered with thousands of structural rearrangements including insertions, deletions, translocation, inversions, duplications, and copy number variations.
Keyur Talsania, Tsai-wei Shen, Xiongfong Chen, Erich Jaeger, Zhipan Li, Zhong Chen, Wanqiu Chen, Bao Tran, Rebecca Kusko, Limin Wang, Andy Wing Chun Pang, Zhaowei Yang, Sulbha Choudhari, Michael Colgan, Li Tai Fang, Andrew Carroll, Jyoti Shetty, Yuliya Kriga, Oksana German, Tatyana Smirnova, Tiantain Liu, Jing Li, Ben Kellman, Karl Hong, Alex R. Hastie, Aparna Natarajan, Ali Moshrefi, Anastasiya Granat, Tiffany Truong, Robin Bombardi, Veronnica Mankinen, Daoud Meerzaman, Christopher E. Mason, Jack Collins, Eric Stahlberg, Chunlin Xiao, Charles Wang, Wenming Xiao, Yongmei Zhao   +38 more
doaj   +1 more source

Best practices for the interpretation and reporting of clinical whole genome sequencing

npj Genomic Medicine, 2022
Whole genome sequencing (WGS) shows promise as a first-tier diagnostic test for patients with rare genetic disorders. However, standards addressing the definition and deployment practice of a best-in-class test are lacking.
Christina A. Austin-Tse, Vaidehi Jobanputra, Denise L. Perry, David Bick, Ryan J. Taft, Eric Venner, Richard A. Gibbs, Ted Young, Sarah Barnett, John W. Belmont, Nicole Boczek, Shimul Chowdhury, Katarzyna A. Ellsworth, Saurav Guha, Shashikant Kulkarni, Cherisse Marcou, Linyan Meng, David R. Murdock, Atteeq U. Rehman, Elizabeth Spiteri, Amanda Thomas-Wilson, Hutton M. Kearney, Heidi L. Rehm, Medical Genome Initiative*   +23 more
doaj   +1 more source

Comparison of illumina and 454 deep sequencing in participants failing raltegravir-based antiretroviral therapy. [PDF]

PLoS ONE, 2014
The impact of raltegravir-resistant HIV-1 minority variants (MVs) on raltegravir treatment failure is unknown. Illumina sequencing offers greater throughput than 454, but sequence analysis tools for viral sequencing are needed.
Jonathan Z Li, Brad Chapman, Patrick Charlebois, Oliver Hofmann, Brian Weiner, Alyssa J Porter, Reshmi Samuel, Saran Vardhanabhuti, Lu Zheng, Joseph Eron, Babafemi Taiwo, Michael C Zody, Matthew R Henn, Daniel R Kuritzkes, Winston Hide, ACTG A5262 Study Team, Cara C Wilson, Baiba I Berzins, Edward P Acosta, Barbara Bastow, Peter S Kim, Sarah W Read, Jennifer Janik, Debra S Meres, Michael M Lederman, Lori Mong-Kryspin, Karl E Shaw, Louis G Zimmerman, Randi Leavitt, Guy De La Rosa, Amy Jennings   +30 more
doaj   +1 more source

Sequence-specific error profile of Illumina sequencers [PDF]

Nucleic Acids Research, 2011
We identified the sequence-specific starting positions of consecutive miscalls in the mapping of reads obtained from the Illumina Genome Analyser (GA). Detailed analysis of the miscall pattern indicated that the underlying mechanism involves sequence-specific interference of the base elongation process during sequencing. The two major sequence patterns
Nakamura, Kensuke, Oshima, Taku, Morimoto, Takuya, Ikeda, Shun, Yoshikawa, Hirofumi, Shiwa, Yuh, Ishikawa, Shu, Linak, Margaret C., Hirai, Aki, Takahashi, Hiroki, Altaf-Ul-Amin, Md., Ogasawara, Naotake, Kanaya, Shigehiko   +12 more
openaire   +2 more sources

Monitoring Error Rates In Illumina Sequencing [PDF]

Journal of Biomolecular Techniques : JBT, 2016
Guaranteeing high-quality next-generation sequencing data in a rapidly changing environment is an ongoing challenge. The introduction of the Illumina NextSeq 500 and the depreciation of specific metrics from Illumina's Sequencing Analysis Viewer (SAV; Illumina, San Diego, CA, USA) have made it more difficult to determine directly the baseline error ...
Leigh J, Manley, Duanduan, Ma, Stuart S, Levine   +2 more
openaire   +2 more sources

Utility of nanopore sequencing for detecting pathogens in bronchoalveolar lavage fluid from pediatric patients with respiratory failure

Journal of Clinical Virology Plus, 2023
RNA viruses are the most frequent pathogens responsible for respiratory infections, particularly in pediatric patients. Next-generation sequencing, represented by Illumina sequencing, is one of the most comprehensive methods for identifying pathogens ...
Makoto Yamaguchi, Kazuhiro Horiba, Kazunori Haruta, Suguru Takeuchi, Takako Suzuki, Yuka Torii, Shinji Kawabe, Sho Wada, Takanari Ikeyama, Yoshinori Ito, Tomoo Ogi, Jun-ichi Kawada   +11 more
doaj   +1 more source

Analysis, optimization and verification of Illumina-generated 16S rRNA gene amplicon surveys. [PDF]

PLoS ONE, 2014
The exploration of microbial communities by sequencing 16S rRNA genes has expanded with low-cost, high-throughput sequencing instruments. Illumina-based 16S rRNA gene sequencing has recently gained popularity over 454 pyrosequencing due to its lower ...
Michael C Nelson, Hilary G Morrison, Jacquelynn Benjamino, Sharon L Grim, Joerg Graf   +4 more
doaj   +1 more source

Review on Illumina Sequencing Technology

Austin Journal of Veterinary Science & Animal Husbandry, 2022
Illumina sequencing process utilizes biochemical methods to determine the correct order of nucleotide bases in a deoxyribonucleic acid. Macromolecule using sequencing-by-synthesis and reversible dye-terminators that enable the identification of single bases are introduced into DNA strands and used to determine the series of base pairs in DNA.
Emiyu K, Lelisa K
openaire   +1 more source

PANDAseq: paired-end assembler for illumina sequences [PDF]

BMC Bioinformatics, 2012
Abstract Background Illumina paired-end reads are used to analyse microbial communities by targeting amplicons of the 16S rRNA gene. Publicly available tools are needed to assemble overlapping paired-end reads while correcting mismatches and uncalled bases; many errors could be corrected to obtain higher sequence ...
Masella Andre P, Bartram Andrea K, Truszkowski Jakub M, Brown Daniel G, Neufeld Josh D   +4 more
openaire   +3 more sources