scholarly journals AURORA: AUtomatic RObustness coveRage Analysis Tool

2013 ◽  
Author(s):  
Angelo Gargantini ◽  
Marco Guarnieri ◽  
Eros Magri
Keyword(s):  
Analysis Tool ◽  
Coverage Analysis

scholarly journals Chanjo: Clincal grade sequence coverage analysis

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 615
Author(s):  
Robin Andeer ◽  
Måns Magnusson ◽  
Anna Wedell ◽  
Henrik Stranneheim
Keyword(s):  
Region Of Interest ◽  
Analysis Tool ◽  
Sequence Coverage ◽  
Report Generation ◽  
Coverage Analysis ◽  
Aggregate Queries ◽  
Set Up ◽  
Easy Integration ◽  
Genomic Regions ◽  
Multiple Samples

Coverage analysis is essential when analysing massive parallel sequencing (MPS) data. The analysis indicates existence of false negatives or positives in a region of interest or poorly covered genomic regions. There are several tools that have excellent performance when doing coverage analysis on a few samples with predefined regions. However, there is no current tool for collecting samples over a longer period of time for aggregated coverage analysis of multiple samples or sequencing methods. Furthermore, current coverage analysis tools do not generate customized coverage reports or enable exploratory coverage analysis without extensive bioinformatic skill and access to the original alignment files. We present Chanjo, a user friendly coverage analysis tool for persistent storage of coverage data, that, accompanied with Chanjo Report, produces coverage reports that summarize coverage data for predefined regions in an elegant manner. Chanjo Report can produce both structured coverage reports and dynamic reports tailored to a subset of genomic regions, coverage cut-offs or samples. Chanjo stores data in an SQL database where thousands of samples can be added over time, which allows for aggregate queries to discover problematic regions. Chanjo is well tested, supports whole exome and genome sequencing, and follows common UNIX standards, allowing for easy integration into existing pipelines. Chanjo is easy to install and operate, and provides a solution for persistent coverage analysis and clinical-grade reporting. It makes it easy to set up a local database and automate the addition of multiple samples and report generation. To our knowledge there is no other tool with matching capabilities. Chanjo handles the common file formats in genetics, such as BED and BAM, and makes it easy to produce PDF coverage reports that are highly valuable for individuals with limited bioinformatic expertise. We believe Chanjo to be a vital tool for clinicians and researchers performing MPS analysis.

A coverage analysis tool for the effectiveness of software testing

1994 ◽  
Vol 43 (4) ◽  
pp. 527-535 ◽  
Author(s):  
M.R. Lyu ◽  
J.R. Horgan ◽  
S. London
Keyword(s):  
Software Testing ◽  
Analysis Tool ◽  
Coverage Analysis

Ethnogeriatrics: Development and Application of the Cohort Analysis Tool

2014 ◽  
Vol 21 (2) ◽  
pp. 37-52
Author(s):  
Melen McBride
Keyword(s):  
Healthcare Professionals ◽  
Cohort Analysis ◽  
Analysis Tool ◽  
Speech Language Pathology ◽  
Clinical Tool ◽  
Research Activities ◽  
Key Concepts ◽  
Practice Teaching ◽  
Language Pathology ◽  
Significant Factors

Ethnogeriatrics is an evolving specialty in geriatric care that focuses on the health and aging issues in the context of culture for older adults from diverse ethnic backgrounds. This article is an introduction to ethnogeriatrics for healthcare professionals including speech-language pathologists (SLPs). This article focuses on significant factors that contributed to the development of ethnogeriatrics, definitions of some key concepts in ethnogeriatrics, introduces cohort analysis as a teaching and clinical tool, and presents applications for speech-language pathology with recommendations for use of cohort analysis in practice, teaching, and research activities.

“I Can See What You’re Saying”: Clinical Utility of Spectral Moment Analysis

2011 ◽  
Vol 21 (2) ◽  
pp. 44-54
Author(s):  
Kerry Callahan Mandulak
Keyword(s):  
Speech Production ◽  
Speech Signal ◽  
Clinical Utility ◽  
Acoustic Analysis ◽  
Moment Analysis ◽  
Analysis Tool ◽  
Spectral Moment ◽  
Clinical Measure ◽  
Perceptual Analysis ◽  
Disordered Speech

Spectral moment analysis (SMA) is an acoustic analysis tool that shows promise for enhancing our understanding of normal and disordered speech production. It can augment auditory-perceptual analysis used to investigate differences across speakers and groups and can provide unique information regarding specific aspects of the speech signal. The purpose of this paper is to illustrate the utility of SMA as a clinical measure for both clinical speech production assessment and research applications documenting speech outcome measurements. Although acoustic analysis has become more readily available and accessible, clinicians need training with, and exposure to, acoustic analysis methods in order to integrate them into traditional methods used to assess speech production.

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