Related Experiment Videos
gVolante for standardizing completeness assessment of genome and transcriptome assemblies
Osamu Nishimura1, Yuichiro Hara1, Shigehiro Kuraku1
1Phyloinformatics Unit, RIKEN Center for Life Science Technologies, Kobe, Hyogo 650-0047, Japan.
Bioinformatics (Oxford, England)
|October 17, 2017
Summary
gVolante is a new web server for assessing the quality of genome and transcriptome assemblies. It uses established pipelines to evaluate completeness and provides a database for comparing assembly quality.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Increasing availability of genomic and transcriptomic data necessitates robust quality assessment tools.
- Existing metrics like N50 provide limited insights into assembly quality.
- Current pipelines for content-based assessment (CEGMA, BUSCO) lack a unified, user-friendly interface.
Purpose of the Study:
- To introduce gVolante, a novel web server for comprehensive sequence assembly quality assessment.
- To provide an integrated platform for utilizing CEGMA and BUSCO pipelines.
- To enable comparison of assembly quality against publicly available data.
Main Methods:
- Development of a web server integrating CEGMA and BUSCO pipelines.
- Implementation of a database storing pre-computed completeness scores for public datasets.
- Inclusion of metrics beyond gene completeness, such as N50 scaffold length.
Main Results:
- gVolante offers on-demand completeness assessment for user-submitted sequence sets.
- The server provides access to a database of pre-computed quality scores for public data.
- Quality assessments consider both gene content and sequence length metrics for multi-faceted evaluation.
Conclusions:
- gVolante serves as a user-friendly, uniform environment for assembly completeness assessment.
- The tool facilitates comparison of assembly quality across different versions and against public resources.
- It enhances the quality control process for genomic and transcriptomic data analysis.