Quality of prokaryote genome assembly: Indispensable issues of factors affecting prokaryote genome assembly quality

Gene ◽  
2012 ◽  
Vol 505 (2) ◽  
pp. 365-367 ◽  
Author(s):  
Adriana R. Carneiro ◽  
Rommel Thiago Jucá Ramos ◽  
Hivana Patricia Melo Barbosa ◽  
Maria Paula C. Schneider ◽  
Debmalya Barh ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Assembly Quality ◽  
Factors Affecting

scholarly journals A comprehensive investigation of metagenome assembly by linked-read sequencing

Microbiome ◽  
2020 ◽  
Vol 8 (1) ◽  
Author(s):  
Lu Zhang ◽  
Xiaodong Fang ◽  
Herui Liao ◽  
Zhenmiao Zhang ◽  
Xin Zhou ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Simulated Data ◽  
Read Depth ◽  
Marginal Effect ◽  
Assembly Quality ◽  
Microbial Genomes ◽  
Long Reads ◽  
Metagenome Assembly ◽  
Dna Fragment

Abstract Background The human microbiota are complex systems with important roles in our physiological activities and diseases. Sequencing the microbial genomes in the microbiota can help in our interpretation of their activities. The vast majority of the microbes in the microbiota cannot be isolated for individual sequencing. Current metagenomics practices use short-read sequencing to simultaneously sequence a mixture of microbial genomes. However, these results are in ambiguity during genome assembly, leading to unsatisfactory microbial genome completeness and contig continuity. Linked-read sequencing is able to remove some of these ambiguities by attaching the same barcode to the reads from a long DNA fragment (10–100 kb), thus improving metagenome assembly. However, it is not clear how the choices for several parameters in the use of linked-read sequencing affect the assembly quality. Results We first examined the effects of read depth (C) on metagenome assembly from linked-reads in simulated data and a mock community. The results showed that C positively correlated with the length of assembled sequences but had little effect on their qualities. The latter observation was corroborated by tests using real data from the human gut microbiome, where C demonstrated minor impact on the sequence quality as well as on the proportion of bins annotated as draft genomes. On the other hand, metagenome assembly quality was susceptible to read depth per fragment (CR) and DNA fragment physical depth (CF). For the same C, deeper CR resulted in more draft genomes while deeper CF improved the quality of the draft genomes. We also found that average fragment length (μFL) had marginal effect on assemblies, while fragments per partition (NF/P) impacted the off-target reads involved in local assembly, namely, lower NF/P values would lead to better assemblies by reducing the ambiguities of the off-target reads. In general, the use of linked-reads improved the assembly for contig N50 when compared to Illumina short-reads, but not when compared to PacBio CCS (circular consensus sequencing) long-reads. Conclusions We investigated the influence of linked-read sequencing parameters on metagenome assembly comprehensively. While the quality of genome assembly from linked-reads cannot rival that from PacBio CCS long-reads, the case for using linked-read sequencing remains persuasive due to its low cost and high base-quality. Our study revealed that the probable best practice in using linked-reads for metagenome assembly was to merge the linked-reads from multiple libraries, where each had sufficient CR but a smaller amount of input DNA.

PDR: a new genome assembly evaluation metric based on genetics concerns

2020 ◽  
Author(s):  
Luyu Xie ◽  
Limsoon Wong
Keyword(s):  
Genome Assembly ◽  
Pairwise Distance ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Assembly Quality ◽  
Genetic Studies ◽  
A Genome ◽  
Assembly Evaluation ◽  
Evaluation Metric

Abstract Motivation Existing genome assembly evaluation metrics provide only limited insight on specific aspects of genome assembly quality, and sometimes even disagree with each other. For better integrative comparison between assemblies, we propose, here, a new genome assembly evaluation metric, Pairwise Distance Reconstruction (PDR). It derives from a common concern in genetic studies, and takes completeness, contiguity, and correctness into consideration. We also propose an approximation implementation to accelerate PDR computation. Results Our results on publicly available datasets affirm PDR’s ability to integratively assess the quality of a genome assembly. In fact, this is guaranteed by its definition. The results also indicated the error introduced by approximation is extremely small and thus negligible. Availabilityand implementation https://github.com/XLuyu/PDR. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals A Comprehensive Investigation of Metagenome Assembly by Linked-Read Sequencing

2020 ◽  
Author(s):  
Lu Zhang ◽  
Xiaodong Fang ◽  
Herui Liao ◽  
Zhenmiao Zhang ◽  
Xin Zhou ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Simulated Data ◽  
Read Depth ◽  
Marginal Effect ◽  
Assembly Quality ◽  
Microbial Genomes ◽  
Long Reads ◽  
Metagenome Assembly ◽  
Dna Fragment

Abstract Background: The human microbiota are complex systems with important roles in our physiological activities and diseases. Sequencing the microbial genomes in the microbiota can help in our interpretation of their activities. The vast majority of the microbes in the microbiota cannot be isolated for individual sequencing. Current metagenomics practices use short-read sequencing to simultaneously sequence a mixture of microbial genomes. However, these results are in ambiguity during genome assembly, leading to unsatisfactory microbial genome completeness and contig continuity. Linked-Read sequencing is able to remove some of these ambiguities by attaching the same barcode to the reads from a long DNA fragment (10kb-100kb), thus improving metagenome assembly. However, it is not clear how the choices for several parameters in the use of Linked-Read sequencing affect the assembly quality.Results: We first examined the effects of read depth (C) on metagenome assembly from linked-reads in simulated data and a mock community. The results showed that C positively correlated with the length of assembled sequences but had little effect on their qualities. The latter observation was corroborated by tests using real data from the human gut microbiome, where C demonstrated minor impact on the sequence quality as well as on the proportion of bins annotated as draft genomes. On the other hand, metagenome assembly quality was susceptible to read depth per fragment (CR), and DNA fragment physical depth (CF). For the same C, deeper CR resulted in more draft genomes while deeper CF improved the quality of the draft genomes. We also found that average fragment length (μFL), had marginal effect on assemblies, while fragments per partition (NF/P) impacted the off-target reads involved in local assembly, namely, lower NF/P values would lead to better assemblies by reducing the ambiguities of the off-target reads. In general, the use of linked-reads improved the assembly for contig N50 when compared to Illumina short-reads, but not when compared to PacBio CCS (circular consensus sequencing) long-reads.Conclusions: We investigated the influence of Linked-Read sequencing parameters on metagenome assembly comprehensively. While the quality of genome assembly from linked-reads cannot rival that from PacBio CCS long-reads, the case for using Linked-Read sequencing remains persuasive due to its low cost and high base-quality. Our study revealed that the probable best practice in using linked-reads for metagenome assembly was to merge the linked-reads from multiple libraries, where each had sufficient CR but a smaller amount of input DNA.

scholarly journals Significantly improving the quality of genome assemblies through curation

GigaScience ◽  
2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Kerstin Howe ◽  
William Chow ◽  
Joanna Collins ◽  
Sarah Pelan ◽  
Damon-Lee Pointon ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Data Generation ◽  
Research Projects ◽  
Automated Assembly ◽  
Assembly Quality ◽  
Assembly Strategy ◽  
Assembly Evaluation ◽  
Assembly Algorithms ◽  
Genome Assemblies

Abstract Genome sequence assemblies provide the basis for our understanding of biology. Generating error-free assemblies is therefore the ultimate, but sadly still unachieved goal of a multitude of research projects. Despite the ever-advancing improvements in data generation, assembly algorithms and pipelines, no automated approach has so far reliably generated near error-free genome assemblies for eukaryotes. Whilst working towards improved datasets and fully automated pipelines, assembly evaluation and curation is actively used to bridge this shortcoming and significantly reduce the number of assembly errors. In addition to this increase in product value, the insights gained from assembly curation are fed back into the automated assembly strategy and contribute to notable improvements in genome assembly quality. We describe our tried and tested approach for assembly curation using gEVAL, the genome evaluation browser. We outline the procedures applied to genome curation using gEVAL and also our recommendations for assembly curation in a gEVAL-independent context to facilitate the uptake of genome curation in the wider community.

Customer’s satisfaction on service quality at Vietnam Technological and Commercial Joint Stock Bank – An Giang Branch

2020 ◽  
Vol 4 (3) ◽  
pp. First
Author(s):  
Tran Minh Hieu ◽  
Nguyen Duong Ngoc Mai Chi
Keyword(s):  
Customer Satisfaction ◽  
Service Quality ◽  
Test Method ◽  
Quality Of Services ◽  
Factors Affecting ◽  
Factors Influencing ◽  
Alpha Reliability ◽  
Survey Results ◽  
Development Orientation

This study applied SERVQUAL scale of Parasuraman et al to measure factors affecting customer satisfaction on service quality at Vietnam Technological and Commercial Joint Stock Bank - An Giang Branch (Techcombank An Giang). The study was conducted to survey 207 customers who have been using the service at Techcombank An Giang. The survey results were analyzed by the Cronbach's Alpha reliability test method, then used Exploratory factor analysis (EFA) to verify and evaluate the scale of service quality. The results of the regression analysis show that customer's satisfaction about service quality at Techcombank An Giang includes four factors: The factor with the highest level is the Empathy with Beta = 0.253, the second of factor is the Responsibility with Beta = 0.248, ranked third in the influence level is the Tangible with Beta = 0.235, and the lowest impact level is the Reliability with Beta = 0.144. The research also uses statistical methods to describe and test the differences of demographic factors with customer's satisfactionon service quality.The analysis results show that there is no difference between customer's satisfaction on service quality and factors such as gender, age, income, number of transaction banks, regular transaction banks, and time to use the service at Techcombank An Giang. Through the research results, the author would like to propose some ideas to improve the quality of services, thereby attracting new customers and importantly, keeping traditional customers because the development orientation of Techcombank is to take care of old customers to cross sell other products of the bank. The Stud results offer a basis for the branch to identify the factors influencing customer satisfaction on their service quality, thereby having an appropriate strategy to improve customer satisfaction.

THE STUDY ON TA VAT WINE PRODUCTION FROM SUGAR PALM (ARENGA PINNATA) SAP

2014 ◽  
Vol 83 (5) ◽  
Author(s):  
Nguyễn Thị Hồng Thu ◽  
Đặng Minh Nhật ◽  
Nguyễn Hoàng Dung
Keyword(s):  
Room Temperature ◽  
Fermentation Process ◽  
Inoculum Size ◽  
Wine Fermentation ◽  
Wine Production ◽  
Factors Affecting ◽  
Natural Fermentation ◽  
Tropical Asia ◽  
Best Parameters

Sugar palm (Arenga pinnata) is a feather palm native to tropical Asia. In Vietnam, it is named Búng Báng or Đoác and grown only on the highlands in the central or northern part of Vietnam. It is utilized for many purposes, especially for Ta Vat wine production - a characteristic and unique product of Co Tu ethnic minority. However, because of the natural fermentation used in the production, the product quality is inconsistent. The purpose of this study was to examine a new procedure of using palm sap for making Ta Vat wine. Some characteristics of the sap, which was collected at Nam Giang district, Quang Nam province are determined, proving the potential of the sap for making wine product. The quality of sap changes quickly at room temperature. At low temperature (4 - 60C), the changes in sap quality are apparently slower. Examining some factors affecting its quality during the wine fermentation process, we determined the best parameters for the fermentation process as follows: inoculum size of 3% with cell density of about 1x108 cells/ml, the addition of the extract from the bark of Ceylon ironwood (Mesua ferrea L.) 4%. Keywords: Arenga pinnata, sap, Ceylon ironwood bark, Mesua ferrea L., wine fermentation.

IMPROVEMENT OF CLASSIFICATION OF FACTORS AFFECTING THE QUALITY OF SILICON CONNECTIONS IN SEWING PRODUCTS

2019 ◽  
pp. 86-88
Author(s):  
R. H. Batirova ◽  
S. S. Tashpulatov ◽  
I. V. Cherunova ◽  
M. A. Mansurova ◽  
S. L. Matismailov
Keyword(s):  
Factors Affecting
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