Results 61 to 70 of about 860,088 (184)

Development of a qPCR assay for Fasciola spp. identification and a deep amplicon sequencing method for differentiation of fluke species in UK livestock.

PLoS Neglected Tropical Diseases
BackgroundTrematode parasites, or flukes, are a significant economic threat to ruminant production worldwide. Traditional diagnostic methods rely on egg sedimentation from faeces, a time-consuming methodology lacking sensitivity and specificity.
Muhammad Abbas, Kezia Kozel, Olukayode Daramola, Nick Selemetas, Qasim Ali, Shoaib Ashraf, Ibrahim Isah, Inaki Deza-Cruz, Sai Fingerhood, Mark W Robinson, Eric R Morgan, Umer Chaudhry, Martha Betson   +12 more
doaj   +1 more source

Metatranscriptomics and Amplicon Sequencing Reveal Mutualisms in Seagrass Microbiomes [PDF]

Frontiers in Microbiology, 2018
Terrestrial plants benefit from many well-understood mutualistic relationships with root- and leaf-associated microbiomes, but relatively little is known about these relationships for seagrass and other aquatic plants. We used 16S rRNA gene amplicon sequencing and metatranscriptomics to assess potential mutualisms between microorganisms and the ...
Byron C. Crump, John M. Wojahn, Fiona Tomas, Fiona Tomas, Ryan S. Mueller   +4 more
openaire   +3 more sources

Amplicon Sequencing Workflow

, 2023
This is the second release of the amplicon sequencing workflow! I updated my name as well as the following: updated how I centered-log ratio transformed my ASV table (with decostand from vegan) added information about using the Taylor et al (2016 ...
Linton Freund
core   +1 more source

Accurate multiplexing and filtering for high-throughput amplicon-sequencing [PDF]

Nucleic Acids Research, 2015
Tagging amplicons with tag sequences appended to PCR primers allow the multiplexing of numerous samples for high-throughput sequencing (HTS). This approach is routinely used in HTS-based diversity analyses, especially in microbial ecology and biomedical diagnostics.
Esling, Philippe, Lejzerowicz, Franck, Pawlowski, Jan   +2 more
openaire   +4 more sources

tidyGenR: tidy multilocus amplicon genotypes in R [PDF]

PeerJ
Multiplexed amplicon sequencing has become an important tool in phylogenetics and conservation genetics. Amplicon sequencing reads need to be processed to get final haplotypes.
Miguel Camacho-Sanchez, Jennifer A. Leonard   +1 more
doaj   +2 more sources

Direct Metatranscriptome RNA-seq and Multiplex RT-PCR Amplicon Sequencing on Nanopore MinION – Promising Strategies for Multiplex Identification of Viable Pathogens in Food

Frontiers in Microbiology, 2020
Viable pathogenic bacteria are major biohazards that pose a significant threat to food safety. Despite the recent developments in detection platforms, multiplex identification of viable pathogens in food remains a major challenge.
Manyun Yang, Alyssa Cousineau, Xiaobo Liu, Yaguang Luo, Daniel Sun, Daniel Sun, Shaohua Li, Shaohua Li, Tingting Gu, Luo Sun, Hayden Dillow, Jack Lepine, Mingqun Xu, Boce Zhang   +13 more
doaj   +1 more source

Benchmarking Bioinformatic Tools for Amplicon-Based Sequencing of Norovirus

Applied and Environmental Microbiology, 2023
In benchmarking bioinformatic pipelines for analyzing high-throughput sequencing (HTS) data sets, we provide method standardization for bioinformatics broadly and specifically for norovirus in situations for which no officially endorsed methods exist at present.
Amy H. Fitzpatrick, Agnieszka Rupnik, Helen O’Shea, Fiona Crispie, Sinéad Keaveney, Paul D. Cotter   +5 more
openaire   +2 more sources

Comparison of 16S rRNA gene amplicon and whole-genome shotgun metagenomic sequencing for subgingival oral microbiome profiling

Journal of Oral Microbiology
Background Periodontitis is a chronic inflammatory disease driven by a dysbiotic subgingival microbiome. While 16S rRNA gene amplicon sequencing is widely used, whole-genome shotgun (WGS) metagenomics is increasingly applied for higher taxonomic and ...
Jung Hwa Park, Jin Chung, Hyo-Jung Lee, Hee Sam Na   +3 more
doaj   +1 more source

Handling of targeted amplicon sequencing data focusing on index hopping and demultiplexing using a nested metabarcoding approach in ecology

Scientific Reports, 2021
High-throughput sequencing platforms are increasingly being used for targeted amplicon sequencing because they enable cost-effective sequencing of large sample sets.
Yasemin Guenay-Greunke, David A. Bohan, Michael Traugott, Corinna Wallinger   +3 more
doaj   +1 more source

S5. ASVs obtained for the 16S rRNA amplicon sequencing

, 2021
Suppplementary Table S5. ASVs obtained for the 16S rRNA amplicon sequencing.
Tatiana Murillo (11674732)
core   +1 more source