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Species Identification and Profiling of Complex Microbial Communities Using Shotgun Illumina Sequencing of 16S rRNA Amplicon Sequences [PDF]

PLoS ONE, 2013
The high throughput and cost-effectiveness afforded by short-read sequencing technologies, in principle, enable researchers to perform 16S rRNA profiling of complex microbial communities at unprecedented depth and resolution. Existing Illumina sequencing
Swee Hoe Ong, Niranjan Nagarajan, Eliza Xin Pei Ho   +2 more
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The Illumina Sequencing Protocol and the NovaSeq 6000 System

2021
The NovaSeq 6000 is a sequencing platform from Illumina that enables the sequencing of short reads with an output up to 6 Tb. The NovaSeq 6000 uses the typical Illumina sequencing workflow based on library preparation, cluster generation by in situ amplification, and sequencing by synthesis. Flexibility is one of the major features of the NovaSeq 6000.
Modi A., Vai S., Caramelli D., Lari M.
openaire   +3 more sources

ANALYSIS OF CONTEXT-DEPENDENT ERRORS FOR ILLUMINA SEQUENCING

Journal of Bioinformatics and Computational Biology, 2012
The new generation of short-read sequencing technologies requires reliable measures of data quality. Such measures are especially important for variant calling. However, in the particular case of SNP calling, a great number of false-positive SNPs may be obtained. One needs to distinguish putative SNPs from sequencing or other errors. We found that not
Irina I. Abnizova, Steven Leonard, Tom Skelly, Andy Brown, David K. Jackson, Marina Gourtovaia, Guoying Qi, Rene te Boekhorst, Nadeem Faruque, Kevin Lewis, Tony Cox 0001   +10 more
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Comparison between MGI and Illumina sequencing platforms for whole genome sequencing

Genes & Genomics, 2021
Illumina next generation sequencing (NGS) systems are the major sequencing platform in worldwide next-generation sequencing market. On the other hand, MGI Tech launched a series of new NGS equipment that promises to deliver high-quality sequencing data faster and at lower prices than Illumina's sequencing instruments.In this study, we compared the ...
Sol A, Jeon, Jong Lyul, Park, Seung-Jin, Park, Jeong Hwan, Kim, Sung-Ho, Goh, Ji-Youn, Han, Seon-Young, Kim   +6 more
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Illumina Sequencing of Bisulfite-Converted DNA Libraries

Cold Spring Harbor Protocols, 2016
Here we describe a standard MethylC-seq protocol using single-read sequencing on an Illumina Genome Analyzer II platform. The protocol involves ligation of methylated sequencing adaptors to sonicated genomic DNA, gel purification, sodium bisulfite conversion, polymerase chain reaction (PCR) amplification, and sequencing.
Paul M, Lizardi, Qin, Yan, Narendra, Wajapeyee   +2 more
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Multiplex Illumina Sequencing Using DNA Barcoding

Current Protocols in Molecular Biology, 2013
AbstractThe amount of sequence obtained by modern sequencing machines greatly exceeds the sequencing depth requirements of many experiments, especially those involving organisms with small genomes. In the interest of economy and efficiency, various strategies have been developed for multiplexing, in which samples are uniquely tagged with short ...
Koon Ho, Wong, Yi, Jin, Zarmik, Moqtaderi   +2 more
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Illumina Sequencing Library Preparation for Highly Multiplexed Target Capture and Sequencing

Cold Spring Harbor Protocols, 2010
INTRODUCTIONThe large amount of DNA sequence data generated by high-throughput sequencing technologies often allows multiple samples to be sequenced in parallel on a single sequencing run. This is particularly true if subsets of the genome are studied rather than complete genomes.
Meyer, M., Kircher, M.
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The Illumina-Solexa Sequencing Protocol for Bacterial Genomes

2015
Based on reversible dye-terminators technology, the Illumina-solexa sequencing platform enables rapid sequencing-by-synthesis (SBS) of large DNA stretches spanning entire genomes, with the latest instruments capable of producing hundreds of gigabases of data in a single sequencing run.
Zhenfei, Hu, Lei, Cheng, Hai, Wang
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Model-based sequential base calling for Illumina sequencing

2010 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), 2010
In this paper, we study the efficacy of a model-based base-calling approach for Illumina's sequencing platforms. In particular, we investigate Genome Analyzer I reads and provide a detailed biochemical model of the sequencing process, incorporating various non-idealities evident in such systems.
Shreepriya Das, Haris Vikalo, Arjang Hassibi   +2 more
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Genome Sequencing of Steroid-Producing Bacteria with Illumina Technology

2017
Illumina technology is widely used for bacterial whole-genome sequencing due to its simplicity, cheapness, reliability, and abundant software for manipulation with raw data. Illumina technology belongs to a second generation of whole genome sequencing that yields great amount of short reads for genome regions. Genomic DNA is fragmented to short pieces.
Victoria Y, Shtratnikova, Mikhail I, Schelkunov, Marina V, Donova   +2 more
openaire   +2 more sources