Results 21 to 30 of about 860,088 (184)

Groundtruthing next-gen sequencing for microbial ecology-biases and errors in community structure estimates from PCR amplicon pyrosequencing [PDF]

, 2012
Analysis of microbial communities by high-throughput pyrosequencing of SSU rRNA gene PCR amplicons has transformed microbial ecology research and led to the observation that many communities contain a diverse assortment of rare taxa-a phenomenon termed ...
Polson, Shawn W., Shawn W. Polson (139348), Craig W. Herbold (139346), Charles K Lee, Ian R McDonald, S Craig Cary, K Eric Wommack, K. Eric Wommack (139352), Charles K. Lee (139341), Ian R. McDonald (139355), Herbold, Craig W., Lee, Charles Kai-Wu, Shawn W Polson, Shannon J. Williamson (38225), Williamson, Shannon J., Cary, S. Craig, S. Craig Cary (133811), Craig W Herbold, Shannon J Williamson, McDonald, Ian R., Wommack, K. Eric   +20 more
core   +1 more source

Reproducibility and quantitation of amplicon sequencing-based detection [PDF]

The ISME Journal, 2011
Abstract To determine the reproducibility and quantitation of the amplicon sequencing-based detection approach for analyzing microbial community structure, a total of 24 microbial communities from a long-term global change experimental site were examined.
Jizhong, Zhou, Liyou, Wu, Ye, Deng, Xiaoyang, Zhi, Yi-Huei, Jiang, Qichao, Tu, Jianping, Xie, Joy D, Van Nostrand, Zhili, He, Yunfeng, Yang   +9 more
openaire   +2 more sources

Multiple approaches for massively parallel sequencing of SARS-CoV-2 genomes directly from clinical samples

Genome Medicine, 2020
Background COVID-19 (coronavirus disease 2019) has caused a major epidemic worldwide; however, much is yet to be known about the epidemiology and evolution of the virus partly due to the scarcity of full-length SARS-CoV-2 (severe acute respiratory ...
Minfeng Xiao, Xiaoqing Liu, Jingkai Ji, Min Li, Jiandong Li, Lin Yang, Wanying Sun, Peidi Ren, Guifang Yang, Jincun Zhao, Tianzhu Liang, Huahui Ren, Tian Chen, Huanzi Zhong, Wenchen Song, Yanqun Wang, Ziqing Deng, Yanping Zhao, Zhihua Ou, Daxi Wang, Jielun Cai, Xinyi Cheng, Taiqing Feng, Honglong Wu, Yanping Gong, Huanming Yang, Jian Wang, Xun Xu, Shida Zhu, Fang Chen, Yanyan Zhang, Weijun Chen, Yimin Li, Junhua Li   +33 more
doaj   +1 more source

Nanoliter-scale next-generation sequencing library-mediated high-throughput 16S rRNA microbial community profiling

BioTechniques, 2020
An ultra-high-throughput workflow for next-generation sequencing library construction at nanoliter scale for amplicon sequencing, termed Smartchip Nanowell Platform for Target Enrichment, was established using a nanodispenser system and a nanoliter-scale
Hui Zhang, Xiangdan Yu, Zhe Zhang, Zhenhua Liu, Cong Tang, Kun Zhao, Shiyan Liu, Yong Sun, Xiang Li, Zijing Xu, Hong Zhang, Keqing Shi, Yan Fu   +12 more
doaj   +1 more source

Grinder: a versatile amplicon and shotgun sequence simulator [PDF]

Nucleic Acids Research, 2012
We introduce Grinder (http://sourceforge.net/projects/biogrinder/), an open-source bioinformatic tool to simulate amplicon and shotgun (genomic, metagenomic, transcriptomic and metatranscriptomic) datasets from reference sequences. This is the first tool to simulate amplicon datasets (e.g. 16S rRNA) widely used by microbial ecologists.
Angly, Florent E., Willner, Dana, Rohwer, Forest, Hugenholtz, Philip, Tyson, Gene W.   +4 more
openaire   +5 more sources

High-quality single amplicon sequencing method for illumina MiSeq platform using pool of ‘N’ (0–10) spacer-linked target specific primers without PhiX spike-in

BMC Genomics, 2023
Background Illumina sequencing platform requires base diversity in the initial 11 cycles for efficient cluster identification and colour matrix estimation. This limitation yields low-quality data for amplicon libraries having homogeneous base composition.
Tejali Naik, Mohak Sharda, Lakshminarayanan C P, Kumar Virbhadra, Awadhesh Pandit   +4 more
doaj   +1 more source

Removing noise from pyrosequenced amplicons [PDF]

, 2011
<b>Background</b><p></p> In many environmental genomics applications a homologous region of DNA from a diverse sample is first amplified by PCR and then sequenced.
Quince, Christopher, Marie Ollier, Decousus, Stephanie, Davenport, Russell J., Christopher Quince, Davenport Russell J, Quince Christopher, Ollier, Marie, Sandrine Viala, Saghir, Nagi,, Uhrhammer, Nancy, Saghir, Nagi, S El, Turnbaugh, Peter, Davenport, Russell J, Turnbaugh, Peter J., Lanzen Anders, Ponelle, Flora, Nancy Uhrhammer, Russell J Davenport, Lanzen, Anders, Uhrhammer, Nancy A., Axel Poulet, Privat, Maud, Peter J Turnbaugh, Maud Privat, Axel Perin, Lafarge, Laurence, Bidet, Yannick, Laurence Lafarge, Stephanie Decousus, Poulet, Axel, Viala, Sandrine, Yannick Bidet, Nagi S. El Saghir, Yves-Jean Bignon, Bignon, Yves-Jean, Turnbaugh Peter J, El-Saghir, Nagi S., Flora Ponelle, Anders Lanzen, Perin, Axel, Bignon, Yves Jean   +41 more
core   +1 more source

AM fungal amplicon sequencing data.

, 2023
AM fungal amplicon sequencing data.
Wei Fu (10707882)
core   +1 more source

Unusual sequence element found at the end of an amplicon. [PDF]

Molecular and Cellular Biology, 1987
In a polyomavirus-transformed rat cell line, designated LPT, the polyomavirus DNA is integrated into a single chromosomal site. Treatment of LPT cells with carcinogens induces amplification of the integrated virus DNA and flanking cellular sequences.
N, Baran, A, Lapidot, H, Manor
openaire   +2 more sources

PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets [PDF]

, 2012
As 16S rRNA gene targeted massively parallel sequencing has become a common tool for microbial diversity investigations, numerous advances have been made to minimize the influence of sequencing and chimeric PCR artifacts through rigorous quality control ...
Lutgarde Raskin (143205), Ameet J. Pinto (143202), Lutgarde Raskin, Pinto Ameet J., Raskin, L., Ameet J Pinto, Raskin Lutgarde, Pinto, A.   +7 more
core   +2 more sources