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Referee: Reference Assembly Quality Scores.

ABSTRACT: Genome assemblies from next-generation sequencing technologies are now an integral part of biological research, but many sequencing and assembly processes are still error-prone. Unfortunately, these errors can propagate to downstream analyses and wreak havoc on results and conclusions. Although such errors are recognized when dealing with diploid genotype data, modern reference assemblies (which are represented as haploid sequences) lack any type of succinct quality assessment for every position. Here we present Referee, a program that uses diploid genotype quality information in order to annotate a haploid assembly with a quality score for every position. Referee aims to provide an assembly with concise quality information on a Phred-like scale in FASTQ format for easy filtering of low-quality sites. Referee also provides output of quality scores in BED format that can be easily visualized as tracks on most genome browsers. Referee is freely available at https://gwct.github.io/referee/.

SUBMITTER: Thomas GWC

PROVIDER: S-EPMC6535810 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature

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Referee: Reference Assembly Quality Scores.

Thomas Gregg W C GWC Hahn Matthew W MW

Genome biology and evolution 20190501 5

Genome assemblies from next-generation sequencing technologies are now an integral part of biological research, but many sequencing and assembly processes are still error-prone. Unfortunately, these errors can propagate to downstream analyses and wreak havoc on results and conclusions. Although such errors are recognized when dealing with diploid genotype data, modern reference assemblies (which are represented as haploid sequences) lack any type of succinct quality assessment for every position ...[more]

PMID: 31028392

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Project description:Sport does not automatically generate educational benefits for players. For a sports field to become a child-friendly educational environment, it is essential that all actors involved in the organization of youth sport take deliberate educational measures. Among these actors are referees, who should be taken into account during the research on the educational value of sport for the youngest. The subject of the present study was handball referees, who interact with the players during matches. Assuming that the referee is an important actor in sport education and that referee-players interactions are the basic mechanism of the referee's educational influence, this study aimed to assess the quality of his or her interactions with players during handball matches for children aged 9 to 12 years. The research was conducted in a group of 25 handball referees who refereed matches of children in the region of Mazowieckie Voivodeship in Poland. The referees surveyed had current licenses issued by the Warsaw-Mazovian Handball Association. To assess the quality of referee-players interactions, the authors' direct observation tool (Referee-Players' Interaction Assessment Scoring System) was used. The educational referee-players interaction was studied in six dimensions: Positive climate, Responsiveness, Behavior management, Proficiency, Instructing, and Communicating. Data were statistically analyzed using chi-squared test, Mann-Whitney U test and exploratory factor analysis (EFA). Cronbach's alpha values were higher than 0.90 in the factors, showing adequate levels of reliability. The results of the research demonstrated that the assessment of the quality of the referee's educational influence on players was neither affected by the referees' experience nor by the outcome of the match. The quality of educational referee-players interactions in five of the six dimensions studied was assessed as average, whereas positive climate was assessed as poor (three-step scale: poor, average, good). If referees are to support coaches and parents in achieving their educational goals, the results indicate areas where they can improve. The research provided empirical evidence that could be used as a basis for the modification of previous training programs for referees developed by local and national sports associations. The referees should be trained to build a positive climate on the sport field, which consists in creating emotional ties with players (physical proximity, social conversation), expressed in an enthusiastic attitude and joy of contacts (smiling, engagement, positive affect reaction, positive comments, respectful and inclusive language, using players first names, listening to players). In addition, referees must be taught to actively monitor players' emotional, cognitive, social, and health needs, as well as to respond to the players' needs and solve problems.

Dataset Information

Referee: Reference Assembly Quality Scores.

Publications

Referee: Reference Assembly Quality Scores.

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