scholarly journals The Bellerophon pipeline, improving de novo transcriptomes and removing chimeras

2018 ◽  
Author(s):  
Jesse Kerkvliet ◽  
Arthur de Fouchier ◽  
Michiel van Wijk ◽  
Astrid T. Groot
Keyword(s):  
Quality Control ◽  
Quality Assessment ◽  
Reference Genome ◽  
Assessment Tool ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Rna Seq ◽  
Quality Assessment Tool ◽  
Chimeric Sequences

AbstractTranscriptome quality control is an important step in RNA-seq experiments. However, the quality of de novo assembled transcriptomes is difficult to assess, due to the lack of reference genome to compare the assembly to. We developed a method to assess and improve the quality of de novo assembled transcriptomes by focusing on the removal of chimeric sequences. These chimeric sequences can be the result of faulty assembled contigs, merging two transcripts into one. The developed method is incorporated into a pipeline, that we named Bellerophon, which is broadly applicable and easy to use. Bellerophon first uses the quality-assessment tool TransRate to indicate the quality, after which it uses a Transcripts Per Million (TPM) filter to remove lowly expressed contigs and CD-HIT-EST to remove highly identical contigs. To validate the quality of this method, we performed three benchmark experiments: 1) a computational creation of chimeras, 2) identification of chimeric contigs in a transcriptome assembly, 3) a simulated RNAseq experiment using a known reference transcriptome. Overall, the Bellerophon pipeline was able to remove between 40 to 91.9% of the chimeras in transcriptome assemblies and removed more chimeric than non-chimeric contigs. Thus, the Bellerophon sequence of filtration steps is a broadly applicable solution to improve transcriptome assemblies.

scholarly journals Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e2988 ◽  
Author(s):  
Cédric Cabau ◽  
Frédéric Escudié ◽  
Anis Djari ◽  
Yann Guiguen ◽  
Julien Bobe ◽  
...  
Keyword(s):  
Reference Genome ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Error Rates ◽  
Rna Seq ◽  
Software Packages ◽  
Redundancy Reduction ◽  
Assembly Pipeline ◽  
Free Open Source

Background De novo transcriptome assembly of short reads is now a common step in expression analysis of organisms lacking a reference genome sequence. Several software packages are available to perform this task. Even if their results are of good quality it is still possible to improve them in several ways including redundancy reduction or error correction. Trinity and Oases are two commonly used de novo transcriptome assemblers. The contig sets they produce are of good quality. Still, their compaction (number of contigs needed to represent the transcriptome) and their quality (chimera and nucleotide error rates) can be improved. Results We built a de novo RNA-Seq Assembly Pipeline (DRAP) which wraps these two assemblers (Trinity and Oases) in order to improve their results regarding the above-mentioned criteria. DRAP reduces from 1.3 to 15 fold the number of resulting contigs of the assemblies depending on the read set and the assembler used. This article presents seven assembly comparisons showing in some cases drastic improvements when using DRAP. DRAP does not significantly impair assembly quality metrics such are read realignment rate or protein reconstruction counts. Conclusion Transcriptome assembly is a challenging computational task even if good solutions are already available to end-users, these solutions can still be improved while conserving the overall representation and quality of the assembly. The de novo RNA-Seq Assembly Pipeline (DRAP) is an easy to use software package to produce compact and corrected transcript set. DRAP is free, open-source and available under GPL V3 license at http://www.sigenae.org/drap.

scholarly journals dnAQET: a framework to compute a consolidated metric for benchmarking quality of de novo assemblies

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Gokhan Yavas ◽  
Huixiao Hong ◽  
Wenming Xiao
Keyword(s):  
Quality Assessment ◽  
Genome Assembly ◽  
Reference Genome ◽  
De Novo ◽  
Quality Score ◽  
De Novo Genome Assembly ◽  
Genome Assemblies ◽  
Reference Genomes ◽  
Better Than

Abstract Background Accurate de novo genome assembly has become reality with the advancements in sequencing technology. With the ever-increasing number of de novo genome assembly tools, assessing the quality of assemblies has become of great importance in genome research. Although many quality metrics have been proposed and software tools for calculating those metrics have been developed, the existing tools do not produce a unified measure to reflect the overall quality of an assembly. Results To address this issue, we developed the de novo Assembly Quality Evaluation Tool (dnAQET) that generates a unified metric for benchmarking the quality assessment of assemblies. Our framework first calculates individual quality scores for the scaffolds/contigs of an assembly by aligning them to a reference genome. Next, it computes a quality score for the assembly using its overall reference genome coverage, the quality score distribution of its scaffolds and the redundancy identified in it. Using synthetic assemblies randomly generated from the latest human genome build, various builds of the reference genomes for five organisms and six de novo assemblies for sample NA24385, we tested dnAQET to assess its capability for benchmarking quality evaluation of genome assemblies. For synthetic data, our quality score increased with decreasing number of misassemblies and redundancy and increasing average contig length and coverage, as expected. For genome builds, dnAQET quality score calculated for a more recent reference genome was better than the score for an older version. To compare with some of the most frequently used measures, 13 other quality measures were calculated. The quality score from dnAQET was found to be better than all other measures in terms of consistency with the known quality of the reference genomes, indicating that dnAQET is reliable for benchmarking quality assessment of de novo genome assemblies. Conclusions The dnAQET is a scalable framework designed to evaluate a de novo genome assembly based on the aggregated quality of its scaffolds (or contigs). Our results demonstrated that dnAQET quality score is reliable for benchmarking quality assessment of genome assemblies. The dnQAET can help researchers to identify the most suitable assembly tools and to select high quality assemblies generated.

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.

Quality Assessment of Clinical Ethics Consultation. Reflection on the Applicability of the Ethics Consultation Quality Assessment Tool

2021 ◽  
Vol 66 (Special Issue) ◽  
pp. 134-134
Author(s):  
Stephan Nadolny ◽  
◽  
Andre Nowak ◽  
Nicolas Heirich ◽  
Jan Schildmann ◽  
...  
Keyword(s):  
Quality Assessment ◽  
Clinical Ethics ◽  
Assessment Tool ◽  
Ethics Consultation ◽  
Process Quality ◽  
Ethical Analysis ◽  
Clinical Ethics Consultation ◽  
Quality Assessment Tool ◽  
Essential Components

"Background. Clinical ethics consultation has been implemented in many health care institutions. Different methods exist for their evaluation. In this paper we present findings from an evaluation of 21 documentation conducted 2019-2020 by means of the Ethics Consultation Quality Assessment Tool (ECQAT). The applicability of the instrument was analyzed based on a) duration of use, b) ease of use, c) comprehensibility of the items. Results. On average, the analysis with the ECQAT takes 11 minutes per protocol. The greatest difficulties in applying the ECQAT arise a) in assessing the counselling-related information and b) in assessing the ethical analysis as well as the recommendations. Here, different demands on the level of detail of the information may lead to different assessments. Furthermore, the transitions of the ethical analysis and the recommendations, which are relevant for the assessment, could not be delimited exactly in parts of the protocols. Discussion. The assessment of documentation represents a limited part of the quality of ethics consultation. In particular, the quality dimensions of the EQAT do not map communicative elements of process quality, which are essential components (if not the core) of ethics consultations. Moreover, the assessment is strongly depending on the format of the protocols, which, depending on the institution, range from a brief overview of the results to a detailed account. Even in light of aforementioned limitations the ECQAT provides an incentive to improve the process quality of (documented) ethics consultation. "

scholarly journals The association between self-efficacy and self-care in essential hypertension: a systematic review

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Felicia Clara Jun Hui Tan ◽  
Prawira Oka ◽  
Hajira Dambha-Miller ◽  
Ngiap Chuan Tan
Keyword(s):  
Systematic Review ◽  
Quality Assessment ◽  
Self Efficacy ◽  
Observational Studies ◽  
Cognitive Theory ◽  
Assessment Tool ◽  
Self Care ◽  
Quality Assessment Tool ◽  
Medium Quality

Abstract Background The successful management of hypertension requires sustained engagement in self-care behaviour such as adhering to medication regimens and diet. Bandura’s Social Cognitive Theory suggests that self-efficacy is a major determinant of engagement in self-care behaviour. Self-efficacy refers to an individual’s belief in their capacity to execute behaviours necessary to produce specific performance attainments. This systematic review of observational studies aims to summarise and evaluate the quality of evidence available to support the association between self-efficacy and engagement in self-care behaviour in hypertension. Methods Searches were performed of the Pubmed, MEDLINE, CINAHL and OpenSIGLE databases from database inception to January 2020. Reference lists and individual journals were also hand searched. Observational studies in English quantifying self-efficacy and self-care behaviour in hypertensive adults were included. The quality of included articles was assessed with the National Institute of Health Quality Assessment Tool for observational studies. Results The literature search identified 102 studies, of which 22 met the inclusion criteria for full-text review. There were 21 studies which reported that higher self-efficacy was associated with engagement in self-care behaviours including medication adherence (n = 9), physical activity (n = 2) and dietary changes (n = 1). Of these, 12 studies were rated as ‘good’ on the quality assessment tool and 10 were ‘fair’. A common limitation in these studies was a lack of objectivity due to their reliance on self-reporting of engagement in self-care behaviour. Conclusion Our review suggests an association between self-efficacy and self-care. However, the evidence supporting this association is of low to medium quality and is limited by heterogeneity. Our findings suggest the need for further well-designed interventional studies to investigate this association.

scholarly journals Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies

2016 ◽  
Author(s):  
Cédric Cabau ◽  
Frédéric Escudié ◽  
Anis Djari ◽  
Yann Guiguen ◽  
Julien Bobe ◽  
...  
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
Error Rates ◽  
Rna Seq ◽  
De Novo Transcriptome ◽  
Software Packages ◽  
Redundancy Reduction ◽  
Assembly Pipeline ◽  
Free Open Source

Background De novo transcriptome assembly of short reads is now a common step in expression analysis of organisms lacking a reference genome sequence. Several software packages are available to perform this task. Even if their results are of good quality it is still possible to improve them in several ways including redundancy reduction or error correction. Trinity and Oases are two commonly used de novo transcriptome assemblers. The contig sets they produce are of good quality. Still, their compaction (number of contigs needed to represent the transcriptome) and their quality (chimera and nucleotide error rates) can be improved. Results We built a de novo RNA-Seq Assembly Pipeline (DRAP) which wraps these two assemblers (Trinity and Oases) in order to improve their results regarding the above-mentioned criteria. DRAP reduces from 1,3 to 15 fold the number of resulting contigs of the assemblies depending on the read set and the assembler used. This article presents seven assembly comparisons showing in some cases drastic improvements when using DRAP. DRAP does not significantly impair assembly quality metrics such are read realignment rate or protein reconstruction counts. Conclusion Transcriptome assembly is a challenging computational task even if good solutions are already available to end-users, these solutions can still be improved while conserving the overall representation and quality of the assembly. The de novo RNA-Seq Assembly Pipeline (DRAP) is an ease to use software package to produce compact and corrected transcript set. DRAP is free, open-source and available at http://www.sigenae.org/drap .

scholarly journals Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies

2016 ◽  
Author(s):  
Cédric Cabau ◽  
Frédéric Escudié ◽  
Anis Djari ◽  
Yann Guiguen ◽  
Julien Bobe ◽  
...  
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
Error Rates ◽  
Rna Seq ◽  
De Novo Transcriptome ◽  
Software Packages ◽  
Redundancy Reduction ◽  
Assembly Pipeline ◽  
Free Open Source

Background De novo transcriptome assembly of short reads is now a common step in expression analysis of organisms lacking a reference genome sequence. Several software packages are available to perform this task. Even if their results are of good quality it is still possible to improve them in several ways including redundancy reduction or error correction. Trinity and Oases are two commonly used de novo transcriptome assemblers. The contig sets they produce are of good quality. Still, their compaction (number of contigs needed to represent the transcriptome) and their quality (chimera and nucleotide error rates) can be improved. Results We built a de novo RNA-Seq Assembly Pipeline (DRAP) which wraps these two assemblers (Trinity and Oases) in order to improve their results regarding the above-mentioned criteria. DRAP reduces from 1,3 to 15 fold the number of resulting contigs of the assemblies depending on the read set and the assembler used. This article presents seven assembly comparisons showing in some cases drastic improvements when using DRAP. DRAP does not significantly impair assembly quality metrics such are read realignment rate or protein reconstruction counts. Conclusion Transcriptome assembly is a challenging computational task even if good solutions are already available to end-users, these solutions can still be improved while conserving the overall representation and quality of the assembly. The de novo RNA-Seq Assembly Pipeline (DRAP) is an ease to use software package to produce compact and corrected transcript set. DRAP is free, open-source and available at http://www.sigenae.org/drap .

scholarly journals Usability as a Premise of Quality

2019 ◽  
Vol 2 (2) ◽  
pp. 57-71
Author(s):  
Irene Tor-Carroggio ◽  
Daniel Segura ◽  
Olga Soler-Vilageliu
Keyword(s):  
Quality Assessment ◽  
Assessment Tool ◽  
Future Research ◽  
Quality Assessment Tool ◽  
Testing Phase ◽  
European Project ◽  
System Usability Scale ◽  
System Usability ◽  
Key Factor

Usability is a key factor when talking about the quality of a product. The System Usability Scale (SUS) is one of the most popular tools to measure usability due to its numerous advantages and, therefore, a very useful quality assessment tool. Originally designed in English, it is available in some other languages, such as Persian and Greek but no validated version in Spanish can be found yet. This paper bridges this gap by describing the process of statistically validating the SUS into Spanish. The results show that our translation of the SUS is reliable, although our modest sample of informants (N = 50) leaves room for improvement and future research. The validation of the SUS is framed within a European project that will use it for its testing phase.

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