Results 51 to 60 of about 133,775 (185)

Spaced seeds improve k-mer-based metagenomic classification [PDF]

, 2015
Metagenomics is a powerful approach to study genetic content of environmental samples that has been strongly promoted by NGS technologies. To cope with massive data involved in modern metagenomic projects, recent tools [4, 39] rely on the analysis of k ...
Brinda, Karel, Kucherov, Gregory, Sykulski, Maciej   +2 more
core   +2 more sources

Development and Validation of a Next-Generation Sequencing Assay for BRCA1 and BRCA2 Variants for the Clinical Laboratory. [PDF]

PLoS ONE, 2015
The objective of this study was to design and validate a next-generation sequencing assay (NGS) to detect BRCA1 and BRCA2 mutations. We developed an assay using random shearing of genomic DNA followed by RNA bait tile hybridization and NGS sequencing on ...
Charles M Strom, Steven Rivera, Christopher Elzinga, Taraneh Angeloni, Sun Hee Rosenthal, Dana Goos-Root, Martin Siaw, Jamie Platt, Cory Braastadt, Linda Cheng, David Ross, Weimin Sun   +11 more
doaj   +1 more source

Reconciliation between operational taxonomic units and species boundaries [PDF]

, 2017
The development of high-throughput sequencing technologies has revolutionised the field of microbial ecology via 16S rRNA gene amplicon sequencing approaches.
Boon, Nico, Kerckhof, Frederiek-Maarten, Leys, Natalie, Monsieurs, Pieter, Mysara, Mohamed, Props, Ruben, Raes, Jeroen, Vandamme, Peter   +7 more
core   +2 more sources

Taxonomy of anaerobic digestion microbiome reveals biases associated with the applied high throughput sequencing strategies [PDF]

, 2018
In the past few years, many studies investigated the anaerobic digestion microbiome by means of 16S rRNA amplicon sequencing. Results obtained from these studies were compared to each other without taking into consideration the followed procedure for ...
Angelidaki, Irini, Campanaro, Stefano, Kougias, Panagiotis G., Treu, Laura, Zhu, Xinyu   +4 more
core   +3 more sources

PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platform [PDF]

, 2015
1. Studying fungal biodiversit y using data generated from Illumina MiSeq sequencing platforms poses a number of bioinformatic challenges with the analysis typically involving a large number of tools for each analytical step from quality filtering to ...
Booth, Tim, Gibbs, Melanie, Griffiths, Robert I., Gweon, Hyun S., Oliver, Anna, Read, Daniel S., Schonrogge, Karsten, Taylor, Joanne   +7 more
core   +1 more source

A quantitative and qualitative comparison of illumina MiSeq and 454 amplicon sequencing for genotyping the highly polymorphic major histocompatibility complex (MHC) in a non-model species

BMC Research Notes, 2017
Background High-throughput sequencing enables high-resolution genotyping of extremely duplicated genes. 454 amplicon sequencing (454) has become the standard technique for genotyping the major histocompatibility complex (MHC) genes in non-model organisms.
Haslina Razali, Emily O’Connor, Anna Drews, Terry Burke, Helena Westerdahl   +4 more
doaj   +1 more source

Whole Genome Sequencing of Influenza A and B Viruses With the MinION Sequencer in the Clinical Setting: A Pilot Study

Frontiers in Microbiology, 2018
Introduction: Whole genome sequencing (WGS) of influenza viruses is important for preparing vaccines and coping with newly emerging viruses. However, WGS is difficult to perform using conventional next-generation sequencers in developing countries, where
Kazuo Imai, Kazuo Imai, Kazuo Imai, Kaku Tamura, Tomomi Tanigaki, Mari Takizawa, Eiko Nakayama, Takahiko Taniguchi, Misako Okamoto, Yasumasa Nishiyama, Norihito Tarumoto, Norihito Tarumoto, Kotaro Mitsutake, Kotaro Mitsutake, Takashi Murakami, Takashi Murakami, Shigefumi Maesaki, Shigefumi Maesaki, Takuya Maeda, Takuya Maeda   +19 more
doaj   +1 more source

Identifying Bacterial Airways Infection in Stable Severe Asthma Using Oxford Nanopore Sequencing Technologies

Microbiology Spectrum, 2022
Previous metagenomic studies in asthma have been limited by inadequate sequencing depth for species-level bacterial identification and by heterogeneity in clinical phenotyping.
Maisha F. Jabeen, Nicholas D. Sanderson, Dona Foster, Derrick W. Crook, Jennifer L. Cane, Catherine Borg, Clare Connolly, Samantha Thulborn, Ian D. Pavord, Paul Klenerman, Teresa L. Street, Timothy S. C. Hinks   +11 more
doaj   +1 more source

Whole-Genome Sequencing of Porcine Epidemic Diarrhea Virus by Illumina MiSeq Platform [PDF]

, 2016
Porcine epidemic diarrhea virus (PEDV) belongs to the genus Alphacoronavirus of the family Coronaviridae. PEDV was identified as an emerging pathogen in US pig populations in 2013. Since then, this virus has been detected in at least 31 states in the USA and has caused significant economic loss to the swine industry.
Wang, Leyi, Stuber, Tod, Camp, Patrick, Robbe-Austerman, Suelee, Zhang, Yan   +4 more
openaire   +1 more source

mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking. [PDF]

, 2016
Mock communities are an important tool for validating, optimizing, and comparing bioinformatics methods for microbial community analysis. We present mockrobiota, a public resource for sharing, validating, and documenting mock community data resources ...
Arron Shiffer, Benjamin Wolfe, Corinne F. Maurice, J. Gregory Caporaso, Jai Ram Rideout, Josh D. Neufeld, Nicholas A. Bokulich, Peter J. Turnbaugh, Rachel J. Dutton, Rob Knight, William G. Mercurio   +10 more
core   +3 more sources