scholarly journals Sequencing error profiles of Illumina sequencing instruments

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Nicholas Stoler ◽  
Anton Nekrutenko
Keyword(s):  
Error Rate ◽  
Sequencing Error ◽  
Sequencing Technology ◽  
Sequence Context ◽  
Sequencing Experiment ◽  
The Difference ◽  
Public Datasets ◽  
Error Profiles ◽  
Sequence Bias

Abstract Sequencing technology has achieved great advances in the past decade. Studies have previously shown the quality of specific instruments in controlled conditions. Here, we developed a method able to retroactively determine the error rate of most public sequencing datasets. To do this, we utilized the overlaps between reads that are a feature of many sequencing libraries. With this method, we surveyed 1943 different datasets from seven different sequencing instruments produced by Illumina. We show that among public datasets, the more expensive platforms like HiSeq and NovaSeq have a lower error rate and less variation. But we also discovered that there is great variation within each platform, with the accuracy of a sequencing experiment depending greatly on the experimenter. We show the importance of sequence context, especially the phenomenon where preceding bases bias the following bases toward the same identity. We also show the difference in patterns of sequence bias between instruments. Contrary to expectations based on the underlying chemistry, HiSeq X Ten and NovaSeq 6000 share notable exceptions to the preceding-base bias. Our results demonstrate the importance of the specific circumstances of every sequencing experiment, and the importance of evaluating the quality of each one.

scholarly journals DEEP-LONG: A Fast and Accurate Aligner for Long RNA-Seq

2020 ◽  
Author(s):  
Li Hou ◽  
Yadong Wang
Keyword(s):  
Alternative Splicing ◽  
Error Rate ◽  
Sequencing Error ◽  
Rna Seq ◽  
Sequencing Technology ◽  
Short Reads ◽  
Sequencing Errors ◽  
Sequencing Error Rate ◽  
Long Reads ◽  
Gene Structures

Abstract BackgroundIn recent years, because of the development of sequencing technology, long reads were widely used in many studies, include transcriptomics studies. Obviously, Long reads have more advantages than short reads. And long reads align also different from short reads align. Until now Lots of tools can process long RNA-Seq, but there still have some problems need to solve. ResultsWe developed Deep-Long to process long RNA-Seq, Deep-Long is a fast and accurate tool. Deep-Long can handle troubles come from complicated gene structures and sequencing errors well, Deep-Long does well especially on alternative splicing and small exons. When sequencing error rate is low, Deep-Long can rapidly get more accurate results. While sequencing error rate rising, Deep-Long will use more time, but still more fast and accurate than most other tools.ConclusionsDeep-Long is an useful tool to align long RNA-Seq to genome, and Deep-Long can find more exons and splices.

scholarly journals Parameter exploration improves the accuracy of long-read genome assembly

2021 ◽  
Author(s):  
Anurag Priyam ◽  
Alicja Witwicka ◽  
Anindita Brahma ◽  
Eckart Stolle ◽  
Yannick Wurm
Keyword(s):  
Genome Assembly ◽  
Reference Genome ◽  
Error Rates ◽  
Fine Tuning ◽  
Sequencing Error ◽  
High Quality ◽  
Long Read ◽  
Genome Assemblies ◽  
Error Profiles

Long-molecule sequencing is now routinely applied to generate high-quality reference genome assemblies. However, datasets differ in repeat composition, heterozygosity, read lengths and error profiles. The assembly parameters that provide the best results could thus differ across datasets. By integrating four complementary and biologically meaningful metrics, we show that simple fine-tuning of assembly parameters can substantially improve the quality of long-read genome assemblies. In particular, modifying estimates of sequencing error rates improves some metrics more than two-fold. We provide a flexible software, CompareGenomeQualities, that automates comparisons of assembly qualities for researchers wanting a straightforward mechanism for choosing among multiple assemblies.

Letter to the Editor: The Continuing Challenge of Evaluating RSD Impairment and Disability

1998 ◽  
Vol 3 (5) ◽  
pp. 8-10
Author(s):  
Robert L. Knobler ◽  
Charles N. Brooks ◽  
Leon H. Ensalada ◽  
James B. Talmage ◽  
Christopher R. Brigham
Keyword(s):  
Disability Evaluation ◽  
Body Part ◽  
Loss Of Function ◽  
Regulatory Requirements ◽  
Major Cardiac Event ◽  
Clinical Scenarios ◽  
Impairment Score ◽  
Occupational Activities ◽  
The Difference

Abstract The author of the two-part article about evaluating reflex sympathetic dystrophy (RSD) responds to criticisms that a percentage impairment score may not adequately reflect the disability of an individual with RSD. The author highlights the importance of recognizing the difference between impairment and disability in the AMA Guides to the Evaluation of Permanent Impairment (AMA Guides): impairment is the loss, loss of use, or derangement of any body part, system, or function; disability is a decrease in or the loss or absence of the capacity to meet personal, social, or occupational demands or to meet statutory or regulatory requirements because of an impairment. The disparity between impairment and disability can be encountered in diverse clinical scenarios. For example, a person's ability to resume occupational activities following a major cardiac event depends on medical, social, and psychological factors, but nonmedical factors appear to present the greatest impediment and many persons do not resume work despite significant improvements in functional capacity. A key requirement according to the AMA Guides is objective documentation, and the author agrees that when physicians consider the disability evaluation of people, more issues than those relating to the percentage loss of function should be considered. More study of the relationships among impairment, disability, and quality of life in patients with RSD are required.

Pengaruh Kualitas Pelayanan Terhadap Kepuasan Pelanggan di Kantor Perusahaan Umum Badan Urusan Logistik Kota Sampit Kabupaten Kotawaringin Timur

2016 ◽  
Vol 2 (2) ◽  
pp. 1-5
Author(s):  
Masrukin Masrukin ◽  
Hermanto Hermanto
Keyword(s):  
Quality Of Service ◽  
Customer Satisfaction ◽  
Service Quality ◽  
Error Rate ◽  
Research Method ◽  
Statistical Test ◽  
Quality Factors ◽  
Public Companies ◽  
Public Company

Customer satisfaction is influenced by service quality factors, this study aims to find out and analyze how much influence the quality of service on customer satisfaction is felt by customers who use the service of Poor Rice (Raskin) at the Office of Public Companies Logistics Agency (Perum BULOG) in Sampit City Regency East Kotawaringin. The research method used in this study is the method of observation, questionnaire/questionnaire and documentation using a Likert scale and the method of determining the sample used is the error rate of 5% as many as 213 samples. Testing the hypothesis used is a statistical test with the formula "Product moment person". The results showed that there was a very strong correlation between Service Quality and Customer Satisfaction of the Office of Public Company of the Logistics Affairs Agency (Perum BULOG) in the District of East Kotawaringin. As much as 0.9968514278 based on the calculation of Pearson Product Moment value.

COMBINATORIAL POLYNOMIALLY COMPUTABLE CHARACTERISTICS OF SUBSTITUTIONS AND THEIR PROPERTIES

2020 ◽  
Vol 7 (2) ◽  
pp. 34-41
Author(s):  
VLADIMIR NIKONOV ◽  
◽  
ANTON ZOBOV ◽  
Keyword(s):  
Mathematical Expectation ◽  
Point Of View ◽  
Small Range ◽  
Computational Point ◽  
Wide Range ◽  
Bijective Function ◽  
The Difference ◽  
Element Base ◽  
Selection Of

The construction and selection of a suitable bijective function, that is, substitution, is now becoming an important applied task, particularly for building block encryption systems. Many articles have suggested using different approaches to determining the quality of substitution, but most of them are highly computationally complex. The solution of this problem will significantly expand the range of methods for constructing and analyzing scheme in information protection systems. The purpose of research is to find easily measurable characteristics of substitutions, allowing to evaluate their quality, and also measures of the proximity of a particular substitutions to a random one, or its distance from it. For this purpose, several characteristics were proposed in this work: difference and polynomial, and their mathematical expectation was found, as well as variance for the difference characteristic. This allows us to make a conclusion about its quality by comparing the result of calculating the characteristic for a particular substitution with the calculated mathematical expectation. From a computational point of view, the thesises of the article are of exceptional interest due to the simplicity of the algorithm for quantifying the quality of bijective function substitutions. By its nature, the operation of calculating the difference characteristic carries out a simple summation of integer terms in a fixed and small range. Such an operation, both in the modern and in the prospective element base, is embedded in the logic of a wide range of functional elements, especially when implementing computational actions in the optical range, or on other carriers related to the field of nanotechnology.

THE INFLUENCE OF TILLAGE SYSTEMS ON THE GROWTH, DEVELOPMENT AND YIELD OF LONG-FLAX

2020 ◽  
Author(s):  
V. Dumych ◽  
Keyword(s):  
Growth And Development ◽  
Field Experiments ◽  
Conservation Tillage ◽  
Mineral Fertilizers ◽  
Tillage Systems ◽  
Yield And Quality ◽  
Tillage System ◽  
The Difference ◽  
Flax Seeds

The purpose of research: to improve the technology of growing flax in the Western region of Ukraine on the basis of the introduction of systems for minimizing tillage, which will increase the yield of trusts and seeds. Research methods: field, laboratory, visual and comparative calculation method. Research results: Field experiments included the study of three tillage systems (traditional, canning and mulching) and determining their impact on growth and development and yields of trusts and flax seeds. The traditional tillage system included the following operations: plowing with a reversible plow to a depth of 27 cm, cultivation with simultaneous harrowing and pre-sowing tillage. The conservation system is based on deep shelfless loosening of the soil and provided for chiseling to a depth of 40 cm, disking to a depth of 15 cm, cultivation with simultaneous harrowing, pre-sowing tillage. During the implementation of the mulching system, disking to a depth of 15 cm, cultivation with simultaneous harrowing and pre-sowing tillage with a combined unit was carried out. Tillage implements and machines were used to perform tillage operations: disc harrow BDVP-3,6, reversible plow PON-5/4, chisel PCh-3, cultivator KPSP-4, pre-sowing tillage unit LK-4. The SZ-3,6 ASTPA grain seeder was used for sowing long flax of the Kamenyar variety. Simultaneously with the sowing of flax seeds, local application of mineral fertilizers (nitroammophoska 2 c/ha) was carried out. The application of conservation tillage allows to obtain the yield of flax trust at the level of 3,5 t/ha, which is 0,4 t/ha (12.9 %) more than from the area of traditional tillage and 0,7 t/ha (25 %) in comparison with mulching. In the area with canning treatment, the seed yield was the highest and amounted to 0,64 t/ha. The difference between this option and traditional and mulching tillage reaches 0,06 t/ha (10,3 %) and 0.10 t/ha (18.5 %), respectively. Conclusions. Preservation tillage, which is based on shelf-free tillage to a depth of 40 cm and disking to a depth of 15 cm has a positive effect on plant growth and development, yield and quality of flax.

Pengaruh ovaprim, aromatase inhibitor, dan hipofisa terhadap kualitas telur ikan Lele Dumbo (Clarias gariepinus)

2017 ◽  
Vol 5 (1) ◽  
Author(s):  
Erwin A. Aziz ◽  
Ockstan Kalesaran
Keyword(s):  
Survival Rate ◽  
Experimental Design ◽  
Aromatase Inhibitor ◽  
Fish Larvae ◽  
Clarias Gariepinus ◽  
Randomized Design ◽  
Completely Randomized Design ◽  
The Difference ◽  
Hatching Eggs

This study aimed to determine the effect of ovaprim hormone, aromatase inhibitor and pituitary on the quality of the catfish eggs (Clarias gariepinus). Experimental Design used was Completely Randomized Design (CRD) with four treatments, each with three replications. Treatment A: ovaprim; treatment B: Aromatase inhibitors, treatment C: hypophysis and treatment D: Control. The results showed that the difference in treatment gave highly significant effect on fertilization and hatching eggs but no significant effect on the survival rate of larvae. Aromatase inhibitor hormone was the best because it provided highly significant effect on fertilization (92.66%), hatchability of eggs (95%), and surviva rate (81.33%) of fish larvae.   Keywords : Clarias gariepinus. Ovaprim, Aromatase Inhibitor, Hypophysis, egg, larvae

Multivariate micropollutants analysis in marine waters

1995 ◽  
Vol 32 (9-10) ◽  
pp. 341-348
Author(s):  
V. Librando ◽  
G. Magazzù ◽  
A. Puglisi
Keyword(s):  
Multivariate Data Analysis ◽  
Partial Least Squares Regression ◽  
Environmental Chemistry ◽  
Sampling Site ◽  
Principal Component ◽  
Least Squares Regression ◽  
Organic Micropollutants ◽  
Suspended Material ◽  
The Difference

The monitoring of water quality today provides a great quantity of data consisting of the values of the parameters measured as a function of time. In the marine environment, and especially in the suspended material, increasing importance is being given to the presence of organic micropollutants, particularly since some are known to be carcinogenic. As the number of measured parameters increases examining the data and their consequent interpretation becomes more difficult. To overcome such difficulties, numerous chemometric techniques have been introduced in environmental chemistry, such as Multivariate Data Analysis (MVDA), Principal Component Analysis (PCA) and Partial Least Squares Regression (PLSR). The use of the first technique in this work has been applied to the interpretation of the quality of Augusta bay, by measuring the concentration of numerous organic micropollutants, together with the classical water pollution parameters, in different sites and at different times. The MVDA has highlighted the difference between various sampling sites whose data were initially thought to be similar. Furthermore, it has allowed a choice of more significant parameters for future monitoring and more suitable sampling site locations.

Non-steady variations of SOD and phosphate release rate due to changes in the quality of the overlying water

2000 ◽  
Vol 42 (3-4) ◽  
pp. 265-272 ◽  
Author(s):  
T. Inoue ◽  
Y. Nakamura ◽  
Y. Adachi
Keyword(s):  
Release Rate ◽  
Oxygen Demand ◽  
Phosphate Concentration ◽  
Sediment Oxygen Demand ◽  
Biochemical Reactions ◽  
Overlying Water ◽  
Phosphate Release ◽  
Do Concentration ◽  
The Difference

A dynamic model, which predicts non-steady variations in the sediment oxygen demand (SOD) and phosphate release rate, has been designed. This theoretical model consists of three diffusion equations with biochemical reactions for dissolved oxygen (DO), phosphate and ferrous iron. According to this model, step changes in the DO concentration and flow velocity produce drastic changes in the SOD and phosphate release rate within 10 minutes. The vigorous response of the SOD and phosphate release rate is caused by the difference in the time scale of diffusion in the water boundary layer and that of the biochemical reactions in the sediment. Secondly, a negative phosphate transfer from water to sediment can even occur under aerobic conditions. This is caused by the decrease in phosphate concentration in the aerobic layer due to adsorption.

Quality-of-Life Measurement in Advanced Cancer: Assessing the Individual

1999 ◽  
Vol 17 (11) ◽  
pp. 3603-3611 ◽  
Author(s):  
Dympna Waldron ◽  
Ciaran A. O'Boyle ◽  
Michael Kearney ◽  
Michael Moriarty ◽  
Desmond Carney
Keyword(s):  
Quality Of Life ◽  
Advanced Cancer ◽  
Internal Validity ◽  
Semistructured Interview ◽  
Incurable Cancer ◽  
Life Measurement ◽  
The Difference ◽  
The Individual ◽  
Very High

PURPOSE: Despite the increasing importance of assessing quality of life (QoL) in patients with advanced cancer, relatively little is known about individual patient's perceptions of the issues contributing to their QoL. The Schedule for the Evaluation of Individual Quality of Life (SEIQoL) and the shorter SEIQoL–Direct Weighting (SEIQoL-DW) assess individualized QoL using a semistructured interview technique. Here we report findings from the first administration of the SEIQoL and SEIQoL-DW to patients with advanced incurable cancer. PATIENTS AND METHODS: QoL was assessed on a single occasion using the SEIQoL and SEIQoL-DW in 80 patients with advanced incurable cancer. RESULTS: All patients were able to complete the SEIQoL-DW, and 78% completed the SEIQoL. Of a possible score of 100, the median QoL global score was as follows: SEIQoL, 61 (range, 24 to 94); SEIQoL-DW, 60.5 (range, 6 to 95). Psychometric data for SEIQoL indicated very high levels of internal consistency (median r = .90) and internal validity (median R2 = 0.88). Patients' judgments of their QoL were unique to the individual. Family concerns were almost universally rated as more important than health, the difference being significant when measured using the SEIQoL-DW (P = .002). CONCLUSION: Patients with advanced incurable cancer were very good judges of their QoL, and many patients rated their QoL as good. Judgments were highly individual, with very high levels of consistency and validity. The primacy given to health in many QoL questionnaires may be questioned in this population. The implications of these findings are discussed with regard to clinical assessment and advance directives.

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