scholarly journals Significantly improving the quality of genome assemblies through curation

2020 ◽  
Author(s):  
Kerstin Howe ◽  
William Chow ◽  
Joanna Collins ◽  
Sarah Pelan ◽  
Damon-Lee Pointon ◽  
...  
Keyword(s):  
Data Sets ◽  
Data Generation ◽  
Research Projects ◽  
Automated Assembly ◽  
Assembly Quality ◽  
Assembly Strategy ◽  
Assembly Evaluation ◽  
Assembly Algorithms ◽  
Genome Assemblies

AbstractBackgroundGenome 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.ResultsWhilst working towards improved data sets and fully automated pipelines, assembly evaluation and curation is actively employed 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.ConclusionsWe 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 an gEVAL-independent context to facilitate the uptake of genome curation in the wider community.

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.

scholarly journals Assessment the Quality of Genome Assemblies by using QUAST Tool for Metagenomics

2020 ◽  
Vol 8 (6) ◽  
pp. 4253-4259
Keyword(s):  
Genome Sequencing ◽  
Reference Genome ◽  
Assessment Tool ◽  
Quality Assessment Tool ◽  
Assembly Evaluation ◽  
Assembly Algorithms ◽  
Genome Assemblies ◽  
Modern Tool ◽  
Assembly Software

Number of assembly algorithms have emerged out but due to constraints of genome sequencing techniques no one is perfect. Various methods for assembler’s comparison have been developed, but none is yet a recognized standard. The problem of evaluating assemblies of formerly unsequenced species has not been considered, because mostly existing methods for comparing assemblies are only applicable to new assemblies of finished genomes. For comparing and evaluating genome assemblies we have used QUAST (Quality Assessment Tool). This tool is used to assess the quality of leading assembly software by evaluating quality metrics. Assemblies with a reference genome, as well as without a reference can be evaluated by QUAST tool. For genome assembly evaluation based on alignment of contigs to a reference, it is a modern tool. In this study we demonstrate QUAST performance by comparing several leading genome assemblers on three metagenomic datasets.

scholarly journals New approaches for metagenome assembly with short reads

2019 ◽  
Vol 21 (2) ◽  
pp. 584-594 ◽  
Author(s):  
Martin Ayling ◽  
Matthew D Clark ◽  
Richard M Leggett
Keyword(s):  
Genome Assembly ◽  
Metagenomic Data ◽  
Data Sets ◽  
New Approaches ◽  
Single Genome ◽  
Metagenome Assembly ◽  
New Type ◽  
Assembly Algorithms ◽  
Genome Assemblies

Abstract In recent years, the use of longer range read data combined with advances in assembly algorithms has stimulated big improvements in the contiguity and quality of genome assemblies. However, these advances have not directly transferred to metagenomic data sets, as assumptions made by the single genome assembly algorithms do not apply when assembling multiple genomes at varying levels of abundance. The development of dedicated assemblers for metagenomic data was a relatively late innovation and for many years, researchers had to make do using tools designed for single genomes. This has changed in the last few years and we have seen the emergence of a new type of tool built using different principles. In this review, we describe the challenges inherent in metagenomic assemblies and compare the different approaches taken by these novel assembly tools.

scholarly journals Assessing species coverage and assembly quality of rapidly accumulating sequenced genomes

2021 ◽  
Author(s):  
Romain Feron ◽  
Robert Michael Waterhouse
Keyword(s):  
Large Scale ◽  
Automated Analysis ◽  
Single Copy ◽  
The United States ◽  
Community Resource ◽  
Assembly Quality ◽  
Sequencing Technologies ◽  
Analysis Workflow ◽  
Genome Assemblies

Ambitious initiatives to coordinate genome sequencing of Earth's biodiversity mean that the accumulation of genomic data is growing rapidly. In addition to cataloguing biodiversity, these data provide the basis for understanding biological function and evolution. Accurate and complete genome assemblies offer a comprehensive and reliable foundation upon which to advance our understanding of organismal biology at genetic, species, and ecosystem levels. However, ever-changing sequencing technologies and analysis methods mean that available data are often heterogeneous in quality. In order to guide forthcoming genome generation efforts and promote efficient prioritisation of resources, it is thus essential to define and monitor taxonomic coverage and quality of the data. Here we present an automated analysis workflow that surveys genome assemblies from the United States National Center for Biotechnology Information (NCBI), assesses their completeness using the relevant Benchmarking Universal Single-Copy Orthologue (BUSCO) datasets, and collates the results into an interactively browsable resource. We apply our workflow to produce a community resource of available assemblies from the phylum Arthropoda, the Arthropoda Assembly Assessment Catalogue. Using this resource, we survey current taxonomic coverage and assembly quality at the NCBI, we examine how key assembly metrics relate to gene content completeness, and we compare results from using different BUSCO lineage datasets. These results demonstrate how the workflow can be used to build a community resource that enables large-scale assessments to survey species coverage and data quality of available genome assemblies, and to guide prioritisations for ongoing and future sampling, sequencing, and genome generation initiatives.

scholarly journals New approaches for assembly of short-read metagenomic data

2018 ◽  
Author(s):  
Martin Ayling ◽  
Matthew D Clark ◽  
Richard M Leggett
Keyword(s):  
Genome Assembly ◽  
Metagenomic Data ◽  
Short Read ◽  
New Approaches ◽  
Single Genome ◽  
New Type ◽  
Multiple Genomes ◽  
Assembly Algorithms ◽  
Genome Assemblies

In recent years, the use of longer-range read data combined with advances in assembly algorithms has stimulated big improvements in the contiguity and quality of genome assemblies. However, these advances have not directly transferred to metagenomic datasets, as assumptions made by the single genome assembly algorithms do not apply when assembling multiple genomes at varying levels of abundance. The development of dedicated assemblers for metagenomic data was a relatively late innovation and for many years, researchers had to make do using tools designed for single genomes. This has changed in the last few years and we have seen the emergence of a new type of tool built using different principles. In this review, we describe the challenges inherent in metagenomic assemblies and compare the different approaches taken by these novel assembly tools.

scholarly journals Quality Assessment of Domesticated Animal Genome Assemblies

2015 ◽  
Vol 9S4 ◽  
pp. BBI.S29333 ◽  
Author(s):  
Stefan E. Seemann ◽  
Christian Anthon ◽  
Oana Palasca ◽  
Jan Gorodkin
Keyword(s):  
High Throughput Sequencing ◽  
Genomic Sequence ◽  
Rna Seq ◽  
Sequencing Data ◽  
Assembly Quality ◽  
High Quality ◽  
Rnaseq Data ◽  
Genome Assemblies ◽  
Animal Genomes

The era of high-throughput sequencing has made it relatively simple to sequence genomes and transcriptomes of individuals from many species. In order to analyze the resulting sequencing data, high-quality reference genome assemblies are required. However, this is still a major challenge, and many domesticated animal genomes still need to be sequenced deeper in order to produce high-quality assemblies. In the meanwhile, ironically, the extent to which RNA seq and other next-generation data is produced frequently far exceeds that of the genomic sequence. Furthermore, basic comparative analysis is often affected by the lack of genomic sequence. Herein, we quantify the quality of the genome assemblies of 20 domesticated animals and related species by assessing a range of measurable parameters, and we show that there is a positive correlation between the fraction of mappable reads from RNAseq data and genome assembly quality. We rank the genomes by their assembly quality and discuss the implications for genotype analyses.

scholarly journals Employing meta-ethnography in the analysis of qualitative data sets on youth activism: a new tool for transnational research projects?

2017 ◽  
Vol 18 (1) ◽  
pp. 108-130 ◽  
Author(s):  
Hilary Pilkington
Keyword(s):  
Qualitative Data ◽  
Youth Activism ◽  
Primary Data ◽  
Data Sets ◽  
European Research ◽  
Research Projects ◽  
Worked Example ◽  
Primary Data Analysis ◽  
Individual Differentiation

This article outlines a novel application of meta-ethnographic synthesis in the analysis of multiple ethnographic case studies of youth activism emanating from a large transnational European research project. Although meta-ethnography is used increasingly as an alternative to systematic review for the synthesis of published qualitative studies, it is not widely applied to the synthesis of primary data. This article suggests such a use is not precluded epistemologically and potentially addresses a growing need as ethnography itself becomes increasingly ‘multi-sited’. The article outlines the practical process of adapting meta-ethnography to primary data analysis drawing on the synthesis of 44 ethnographic cases of youth activism and provides a worked example of the translation of cases and resulting ‘line of argument’. It discusses the challenges and limitations of the approach in particular the danger that, in extracting the general from the specific, the key quality of qualitative data – individual differentiation – is diminished.

scholarly journals New approaches for assembly of short-read metagenomic data

2018 ◽  
Author(s):  
Martin Ayling ◽  
Matthew D Clark ◽  
Richard M Leggett
Keyword(s):  
Genome Assembly ◽  
Metagenomic Data ◽  
Short Read ◽  
New Approaches ◽  
Single Genome ◽  
New Type ◽  
Multiple Genomes ◽  
Assembly Algorithms ◽  
Genome Assemblies

In recent years, the use of longer-range read data combined with advances in assembly algorithms has stimulated big improvements in the contiguity and quality of genome assemblies. However, these advances have not directly transferred to metagenomic datasets, as assumptions made by the single genome assembly algorithms do not apply when assembling multiple genomes at varying levels of abundance. The development of dedicated assemblers for metagenomic data was a relatively late innovation and for many years, researchers had to make do using tools designed for single genomes. This has changed in the last few years and we have seen the emergence of a new type of tool built using different principles. In this review, we describe the challenges inherent in metagenomic assemblies and compare the different approaches taken by these novel assembly tools.

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.

Trust in the Police: Cross-country Comparisons

2012 ◽  
pp. 24-47
Author(s):  
V. Gimpelson ◽  
G. Monusova
Keyword(s):  
Public Opinion ◽  
Public Attitudes ◽  
Crime Rates ◽  
Authoritarian Regimes ◽  
Data Sets ◽  
The Public ◽  
Positive Attitudes ◽  
Cross Country ◽  
Police Activity

Using different cross-country data sets and simple econometric techniques we study public attitudes towards the police. More positive attitudes are more likely to emerge in the countries that have better functioning democratic institutions, less prone to corruption but enjoy more transparent and accountable police activity. This has a stronger impact on the public opinion (trust and attitudes) than objective crime rates or density of policemen. Citizens tend to trust more in those (policemen) with whom they share common values and can have some control over. The latter is a function of democracy. In authoritarian countries — “police states” — this tendency may not work directly. When we move from semi-authoritarian countries to openly authoritarian ones the trust in the police measured by surveys can also rise. As a result, the trust appears to be U-shaped along the quality of government axis. This phenomenon can be explained with two simple facts. First, publicly spread information concerning police activity in authoritarian countries is strongly controlled; second, the police itself is better controlled by authoritarian regimes which are afraid of dangerous (for them) erosion of this institution.

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