scholarly journals Atropos: specific, sensitive, and speedy trimming of sequencing reads

2017 ◽  
Author(s):  
John P Didion ◽  
Marcel Martin ◽  
Francis S Collins
Keyword(s):  
High Performance ◽  
State Of The Art ◽  
Leading Edge ◽  
High Sensitivity ◽  
High Accuracy ◽  
Free Software ◽  
Short Read Sequencing ◽  
Sequencing Errors ◽  
Quality And Reliability ◽  
Broad Feature

A key step in the transformation of raw sequencing reads into biological insights is the trimming of adapter sequences and low-quality bases. Read trimming has been shown to increase the quality and reliability while decreasing the computational requirements of downstream analyses. Many read trimming software tools are available; however, no tool simultaneously provides the accuracy, computational efficiency, and feature set required to handle the types and volumes of data generated in modern sequencing-based experiments. Here we introduce Atropos and show that it trims reads with high sensitivity and specificity while maintaining leading-edge speed. Compared to other state-of-the-art read trimming tools, Atropos achieves significant increases in trimming accuracy while remaining competitive in execution times. Furthermore, Atropos maintains high accuracy even when trimming data with elevated rates of sequencing errors. The accuracy, high performance, and broad feature set offered by Atropos makes it an appropriate choice for the pre-processing of Illumina, ABI SOLiD, and other current-generation short-read sequencing datasets. Availability. Atropos is open source and free software written in Python (3.3+) and available at https://github.com/jdidion/atropos.

scholarly journals Atropos: specific, sensitive, and speedy trimming of sequencing reads

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3720 ◽  
Author(s):  
John P. Didion ◽  
Marcel Martin ◽  
Francis S. Collins
Keyword(s):  
High Performance ◽  
State Of The Art ◽  
Leading Edge ◽  
High Sensitivity ◽  
High Accuracy ◽  
Free Software ◽  
Short Read Sequencing ◽  
Sequencing Errors ◽  
Quality And Reliability ◽  
Broad Feature

A key step in the transformation of raw sequencing reads into biological insights is the trimming of adapter sequences and low-quality bases. Read trimming has been shown to increase the quality and reliability while decreasing the computational requirements of downstream analyses. Many read trimming software tools are available; however, no tool simultaneously provides the accuracy, computational efficiency, and feature set required to handle the types and volumes of data generated in modern sequencing-based experiments. Here we introduce Atropos and show that it trims reads with high sensitivity and specificity while maintaining leading-edge speed. Compared to other state-of-the-art read trimming tools, Atropos achieves significant increases in trimming accuracy while remaining competitive in execution times. Furthermore, Atropos maintains high accuracy even when trimming data with elevated rates of sequencing errors. The accuracy, high performance, and broad feature set offered by Atropos makes it an appropriate choice for the pre-processing of Illumina, ABI SOLiD, and other current-generation short-read sequencing datasets. Atropos is open source and free software written in Python (3.3+) and available at https://github.com/jdidion/atropos.

scholarly journals Atropos: specific, sensitive, and speedy trimming of sequencing reads

2017 ◽  
Author(s):  
John P Didion ◽  
Marcel Martin ◽  
Francis S Collins
Keyword(s):  
High Performance ◽  
State Of The Art ◽  
Leading Edge ◽  
High Sensitivity ◽  
High Accuracy ◽  
Free Software ◽  
Short Read Sequencing ◽  
Sequencing Errors ◽  
Quality And Reliability ◽  
Broad Feature

A key step in the transformation of raw sequencing reads into biological insights is the trimming of adapter sequences and low-quality bases. Read trimming has been shown to increase the quality and reliability while decreasing the computational requirements of downstream analyses. Many read trimming software tools are available; however, no tool simultaneously provides the accuracy, computational efficiency, and feature set required to handle the types and volumes of data generated in modern sequencing-based experiments. Here we introduce Atropos and show that it trims reads with high sensitivity and specificity while maintaining leading-edge speed. Compared to other state-of-the-art read trimming tools, Atropos achieves significant increases in trimming accuracy while remaining competitive in execution times. Furthermore, Atropos maintains high accuracy even when trimming data with elevated rates of sequencing errors. The accuracy, high performance, and broad feature set offered by Atropos makes it an appropriate choice for the pre-processing of Illumina, ABI SOLiD, and other current-generation short-read sequencing datasets. Availability. Atropos is open source and free software written in Python (3.3+) and available at https://github.com/jdidion/atropos.

scholarly journals Atropos: specific, sensitive, and speedy trimming of sequencing reads

2016 ◽  
Author(s):  
John P Didion ◽  
Francis S Collins
Keyword(s):  
High Performance ◽  
Simulated Data ◽  
Leading Edge ◽  
High Sensitivity ◽  
Fold Increase ◽  
Parallel Execution ◽  
High Rate ◽  
Data Sets ◽  
Sequencing Data ◽  
Broad Feature

A key step in the transformation of raw sequencing reads into biological insights is the trimming of adapter sequences and low-quality bases. Read trimming has been shown to increase the quality and reliability while decreasing the computational requirements of downstream analyses. Many read trimming software tools are available; however, no tool simultaneously provides the accuracy, computational efficiency, and feature set required to handle the types and volumes of data generated in modern sequencing-based experiments. Here we introduce Atropos and show that it trims reads with high sensitivity and specificity while maintaining leading-edge speed. Compared to other state-of-the-art read trimming tools, Atropos achieves a four-fold increase in trimming accuracy and a decrease in execution time of ~50% (using 16 parallel execution threads). Furthermore, Atropos maintains high accuracy even when trimming simulated data with a high rate of error. The accuracy, high performance, and broad feature set offered by Atropos makes it an appropriate choice for the pre-processing of most current-generation sequencing data sets. Atropos is open source and free software written in Python and available at https://github.com/jdidion/atropos.

scholarly journals Atropos: specific, sensitive, and speedy trimming of sequencing reads

2017 ◽  
Author(s):  
John P Didion ◽  
Marcel Martin ◽  
Francis S Collins
Keyword(s):  
High Performance ◽  
Simulated Data ◽  
Leading Edge ◽  
High Sensitivity ◽  
Fold Increase ◽  
Parallel Execution ◽  
High Rate ◽  
Data Sets ◽  
Sequencing Data ◽  
Broad Feature

A key step in the transformation of raw sequencing reads into biological insights is the trimming of adapter sequences and low-quality bases. Read trimming has been shown to increase the quality and reliability while decreasing the computational requirements of downstream analyses. Many read trimming software tools are available; however, no tool simultaneously provides the accuracy, computational efficiency, and feature set required to handle the types and volumes of data generated in modern sequencing-based experiments. Here we introduce Atropos and show that it trims reads with high sensitivity and specificity while maintaining leading-edge speed. Compared to other state-of-the-art read trimming tools, Atropos achieves a four-fold increase in trimming accuracy and a decrease in execution time of ~50% (using 16 parallel execution threads). Furthermore, Atropos maintains high accuracy even when trimming simulated data with a high rate of error. The accuracy, high performance, and broad feature set offered by Atropos makes it an appropriate choice for the pre-processing of most current-generation sequencing data sets. Atropos is open source and free software written in Python and available at https://github.com/jdidion/atropos.

scholarly journals Atropos: specific, sensitive, and speedy trimming of sequencing reads

2016 ◽  
Author(s):  
John P Didion ◽  
Francis S Collins
Keyword(s):  
High Performance ◽  
Simulated Data ◽  
Leading Edge ◽  
High Sensitivity ◽  
Fold Increase ◽  
Parallel Execution ◽  
High Rate ◽  
Data Sets ◽  
Sequencing Data ◽  
Broad Feature

A key step in the transformation of raw sequencing reads into biological insights is the trimming of adapter sequences and low-quality bases. Read trimming has been shown to increase the quality and reliability while decreasing the computational requirements of downstream analyses. Many read trimming software tools are available; however, no tool simultaneously provides the accuracy, computational efficiency, and feature set required to handle the types and volumes of data generated in modern sequencing-based experiments. Here we introduce Atropos and show that it trims reads with high sensitivity and specificity while maintaining leading-edge speed. Compared to other state-of-the-art read trimming tools, Atropos achieves a four-fold increase in trimming accuracy and a decrease in execution time of ~50% (using 16 parallel execution threads). Furthermore, Atropos maintains high accuracy even when trimming simulated data with a high rate of error. The accuracy, high performance, and broad feature set offered by Atropos makes it an appropriate choice for the pre-processing of most current-generation sequencing data sets. Atropos is open source and free software written in Python and available at https://github.com/jdidion/atropos.

Special Issue on High Performance Cutting and Related Manufacturing Technologies

2011 ◽  
Vol 5 (3) ◽  
pp. 269-269
Author(s):  
Tojiro Aoyama
Keyword(s):  
Working Group ◽  
High Performance ◽  
State Of The Art ◽  
Leading Edge ◽  
Special Issue ◽  
Editorial Committee ◽  
International Conference ◽  
Convention Center ◽  
Manufacturing Technologies ◽  
Conference Papers

The 4th CIRP International Conference on High Performance Cutting had been held at the Nagaragawa Convention Center in Gifu City of Japan in October 2010. The scope of the conference was to review and discuss the visions, state of the art and innovations in the area of high performance cutting and related manufacturing technologies. This conference is originated from the CIRP Working Group in High Performance Cutting established by Professor G. Byrne in 2001. After four workshops in Europe, the 1st international conference on HPC was held in Aachen in 2004 chaired by Professor Byrne and Professor F. Klocke. The second one was held in Vancouver under the chairmanship of Professor Y. Altintas and the 3rd one was organized by Professor Byrne and Dr. O’connell in Dublin. In this conference, 144 interesting papers were presented from 19 countries. The editorial committee of IJAT selected the excellent papers presented at the conference and requested the authors to contribute manuscripts in expanded version of conference papers. As a result, 25 papers were accepted for the publication. I believe that this special issue provides the readers valuable information at the leading edge of manufacturing technologies. I would like to express my sincere appreciation to all of the authors and reviewers for their invaluable effort.

Determination of Selected Phthalates in Some Commercial Cosmetic Products by HPLC-UV

2020 ◽  
Vol 23 (10) ◽  
pp. 1010-1022
Author(s):  
Emrah Dural
Keyword(s):  
High Performance ◽  
Phthalate Esters ◽  
High Sensitivity ◽  
Hplc Method ◽  
Cosmetic Products ◽  
Limit Of Quantification ◽  
Nail Polish ◽  
Accuracy And Precision ◽  
Butyl Phthalate

Aim and scope: Due to the serious toxicological risks and their widespread use, quantitative determination of phthalates in cosmetic products have importance for public health. The aim of this study was to develop a validated simple, rapid and reliable high-performance liquid chromatography (HPLC) method for the determination of phthalates which are; dimethyl phthalate (DMP), diethyl phthalate (DEP), benzyl butyl phthalate (BBP), di-n-butyl phthalate (DBP), di(2- ethylhexyl) phthalate (DEHP), in cosmetic products and to investigate these phthalate (PHT) levels in 48 cosmetic products marketing in Sivas, Turkey. Materials and Methods: Separation was achieved by a reverse-phase ACE-5 C18 column (4.6 x 250 mm, 5.0 μm). As the mobile phase, 5 mM KH2PO4 and acetonitrile were used gradiently at 1.5 ml min-1. All PHT esters were detected at 230 nm and the run time was taking 21 minutes. Results: This method showed the high sensitivity value the limit of quantification (LOQ) values for which are below 0.64 μg mL-1 of all phthalates. Method linearity was ≥0.999 (r2). Accuracy and precision values of all phthalates were calculated between (-6.5) and 6.6 (RE%) and ≤6.2 (RSD%), respectively. Average recovery was between 94.8% and 99.6%. Forty-eight samples used for both babies and adults were successfully analyzed by the developed method. Results have shown that, DMP (340.7 μg mL-1 ±323.7), DEP (1852.1 μg mL-1 ± 2192.0), and DBP (691.3 μg mL-1 ± 1378.5) were used highly in nail polish, fragrance and cream products, respectively. Conclusion: Phthalate esters, which are mostly detected in the content of fragrance, cream and nail polish products and our research in general, are DEP (1852.1 μg mL-1 ± 2192.0), DBP (691.3 μg mL-1 ± 1378.5) and DMP (340.7 μg mL-1 ±323.7), respectively. Phthalates were found in the content of all 48 cosmetic products examined, and the most detected phthalates in general average were DEP (581.7 μg mL-1 + 1405.2) with a rate of 79.2%. The unexpectedly high phthalate content in the examined cosmetic products revealed a great risk of these products on human health. The developed method is a simple, sensitive, reliable and economical alternative for the determination of phthalates in the content of cosmetic products, it can be used to identify phthalate esters in different products after some modifications.

scholarly journals Design of a Sensitive Balloon Sensor for Safe Human–Robot Interaction

Sensors ◽  
2021 ◽  
Vol 21 (6) ◽  
pp. 2163
Author(s):  
Dongjin Kim ◽  
Seungyong Han ◽  
Taewi Kim ◽  
Changhwan Kim ◽  
Doohoe Lee ◽  
...  
Keyword(s):  
High Performance ◽  
Strain Sensor ◽  
High Sensitivity ◽  
Human Robot Interaction ◽  
Large Area ◽  
Tactile Sensors ◽  
Robot Interaction ◽  
Mechanical Crack ◽  
Flexible Strain Sensor ◽  
Contact Sensing

As the safety of a human body is the main priority while interacting with robots, the field of tactile sensors has expanded for acquiring tactile information and ensuring safe human–robot interaction (HRI). Existing lightweight and thin tactile sensors exhibit high performance in detecting their surroundings. However, unexpected collisions caused by malfunctions or sudden external collisions can still cause injuries to rigid robots with thin tactile sensors. In this study, we present a sensitive balloon sensor for contact sensing and alleviating physical collisions over a large area of rigid robots. The balloon sensor is a pressure sensor composed of an inflatable body of low-density polyethylene (LDPE), and a highly sensitive and flexible strain sensor laminated onto it. The mechanical crack-based strain sensor with high sensitivity enables the detection of extremely small changes in the strain of the balloon. Adjusting the geometric parameters of the balloon allows for a large and easily customizable sensing area. The weight of the balloon sensor was approximately 2 g. The sensor is employed with a servo motor and detects a finger or a sheet of rolled paper gently touching it, without being damaged.

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