scholarly journals ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data

2009 ◽  
Vol 25 (19) ◽  
pp. 2607-2608 ◽  
Author(s):  
M. Morgan ◽  
S. Anders ◽  
M. Lawrence ◽  
P. Aboyoun ◽  
H. Pages ◽  
...  
Keyword(s):  
Quality Assessment ◽  
High Throughput ◽  
Sequence Data ◽  
Bioconductor Package ◽  
Input Quality

scholarly journals Hill number as a bacterial diversity measure framework with high-throughput sequence data

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Sanghoon Kang ◽  
Jorge L. M. Rodrigues ◽  
Justin P. Ng ◽  
Terry J. Gentry
Keyword(s):  
Bacterial Diversity ◽  
High Throughput ◽  
Sequence Data ◽  
Diversity Measure ◽  
Hill Number

Two-Level Parallel Alignment Based on Sequence Parallel Vectorization

2014 ◽  
Vol 490-491 ◽  
pp. 757-762
Author(s):  
Guo Li Ji ◽  
Long Teng Chen ◽  
Liang Liang Chen
Keyword(s):  
T Cell ◽  
T Cell Receptor ◽  
Sequence Alignment ◽  
High Throughput ◽  
Sequence Data ◽  
Cell Receptor ◽  
Alignment Accuracy ◽  
Gpu Acceleration ◽  
Alignment Algorithm ◽  
Alignment Result

This paper proposed a way of two-level parallel alignment based on sequence parallel vectorization with GPU acceleration on the Fermi architecture, which integrates sequence parallel vectorization, parallel k-means clustering approximate alignment and parallel Smith-Waterman algorithm. The method converts sequence alignment into vector alignment by first. Then it uses k-means alignment to divide sequences into several groups and reduce the size of sequence data. The expected accurate alignment result is achieved using parallel Smith-Waterman algorithm. The high-throughput mouse T-cell receptor (TCR) sequences were used to validate the proposed method. Under the same hardware condition, comparing to serial Smith-Waterman algorithm and CUDASW++2.0 algorithm, our method is the most efficient alignment algorithm with high alignment accuracy.

scholarly journals Publisher Correction: Optimal compressed representation of high throughput sequence data via light assembly

2018 ◽  
Vol 9 (1) ◽  
Author(s):  
Antonio A. Ginart ◽  
Joseph Hui ◽  
Kaiyuan Zhu ◽  
Ibrahim Numanagić ◽  
Thomas A. Courtade ◽  
...  
Keyword(s):  
High Throughput ◽  
Sequence Data

scholarly journals High-Throughput Chemometric Quality Assessment of Extra Virgin Olive Oils Using a Microtiter Plate Reader

Sensors ◽  
2019 ◽  
Vol 19 (19) ◽  
pp. 4169
Author(s):  
Huihui He ◽  
Weiying Lu
Keyword(s):  
Quality Assessment ◽  
High Throughput ◽  
Latent Variables ◽  
Scatter Correction ◽  
Principal Component ◽  
Microtiter Plate ◽  
Food Ingredients ◽  
Virgin Olive Oils ◽  
Olive Oils ◽  
Plate Reader

A commercially available microtiter plate reader was applied as a high-throughput counterpart of ultraviolet-visible (UV–Vis) spectrophotometer to identify the producing location of extra virgin olive oils (EVOOs). Multiplicative scatter correction and the first derivative was used to denoise the UV–Vis spectra and eliminate the effects of background drift. The spectra were analyzed using chemometrics methods including the principal component analysis (PCA) and the partial least squares-discriminant analysis (PLS-DA). The PLS-DA model on full spectra using 5 latent variables showed a classification accuracy of 97.92% by cross-validation. The overall results demonstrated that the use of a UV–Vis spectrophotometer based on the microtiter plate reader combined with chemometrics can be applied to the quality assessment of EVOOs. It is demonstrated that the microtiter plate reader can be a high-throughput tool in the quality assessment of food ingredients.

scholarly journals Comprehensive pathogen detection in sera of Kawasaki disease patients by high-throughput sequencing: a retrospective exploratory study

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Yuka Torii ◽  
Kazuhiro Horiba ◽  
Satoshi Hayano ◽  
Taichi Kato ◽  
Takako Suzuki ◽  
...  
Keyword(s):  
Kawasaki Disease ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Sequence Data ◽  
Early Stage ◽  
Rna Virus ◽  
Systemic Vasculitis ◽  
Human Herpesvirus ◽  
Acute Stage ◽  
Serum Samples

Abstract Background Kawasaki disease (KD) is an idiopathic systemic vasculitis that predominantly damages coronary arteries in children. Various pathogens have been investigated as triggers for KD, but no definitive causative pathogen has been determined. As KD is diagnosed by symptoms, several days are needed for diagnosis. Therefore, at the time of diagnosis of KD, the pathogen of the trigger may already be diminished. The aim of this study was to explore comprehensive pathogens in the sera at the acute stage of KD using high-throughput sequencing (HTS). Methods Sera of 12 patients at an extremely early stage of KD and 12 controls were investigated. DNA and RNA sequences were read separately using HTS. Sequence data were imported into the home-brew meta-genomic analysis pipeline, PATHDET, to identify the pathogen sequences. Results No RNA virus reads were detected in any KD case except for that of equine infectious anemia, which is known as a contaminant of commercial reverse transcriptase. Concerning DNA viruses, human herpesvirus 6B (HHV-6B, two cases) and Anelloviridae (eight cases) were detected among KD cases as well as controls. Multiple bacterial reads were obtained from KD and controls. Bacteria of the genera Acinetobacter, Pseudomonas, Delfita, Roseomonas, and Rhodocyclaceae appeared to be more common in KD sera than in the controls. Conclusion No single pathogen was identified in serum samples of patients at the acute phase of KD. With multiple bacteria detected in the serum samples, it is difficult to exclude the possibility of contamination; however, it is possible that these bacteria might stimulate the immune system and induce KD.

scholarly journals Focus Quality Assessment of High-Throughput Whole Slide Imaging in Digital Pathology

2020 ◽  
Vol 39 (1) ◽  
pp. 62-74 ◽  
Author(s):  
Mahdi S. Hosseini ◽  
Jasper A. Z. Brawley-Hayes ◽  
Yueyang Zhang ◽  
Lyndon Chan ◽  
Konstantinos Plataniotis ◽  
...  
Keyword(s):  
Quality Assessment ◽  
High Throughput ◽  
Digital Pathology ◽  
Whole Slide Imaging

scholarly journals High-Throughput Crystallization Pipeline at the Crystallography Core Facility of the Institut Pasteur

Molecules ◽  
2019 ◽  
Vol 24 (24) ◽  
pp. 4451 ◽  
Author(s):  
Patrick Weber ◽  
Cédric Pissis ◽  
Rafael Navaza ◽  
Ariel E. Mechaly ◽  
Frederick Saul ◽  
...  
Keyword(s):  
High Throughput ◽  
Sequence Data ◽  
Data Bank ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
X Ray Diffraction ◽  
Sequencing Technology ◽  
X Ray ◽  
Set Up ◽  
General User

The availability of whole-genome sequence data, made possible by significant advances in DNA sequencing technology, led to the emergence of structural genomics projects in the late 1990s. These projects not only significantly increased the number of 3D structures deposited in the Protein Data Bank in the last two decades, but also influenced present crystallographic strategies by introducing automation and high-throughput approaches in the structure-determination pipeline. Today, dedicated crystallization facilities, many of which are open to the general user community, routinely set up and track thousands of crystallization screening trials per day. Here, we review the current methods for high-throughput crystallization and procedures to obtain crystals suitable for X-ray diffraction studies, and we describe the crystallization pipeline implemented in the medium-scale crystallography platform at the Institut Pasteur (Paris) as an example.

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