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. 2017 Nov 15;33(22):3635-3637.
doi: 10.1093/bioinformatics/btx445.

gVolante for standardizing completeness assessment of genome and transcriptome assemblies

Osamu Nishimura  1 , Yuichiro Hara  1 , Shigehiro Kuraku  1
Affiliations

gVolante for standardizing completeness assessment of genome and transcriptome assemblies

Osamu Nishimura et al. Bioinformatics. .

Abstract

Motivation: Along with the increasing accessibility to comprehensive sequence information, such as whole genomes and transcriptomes, the demand for assessing their quality has been multiplied. To this end, metrics based on sequence lengths, such as N50, have become a standard, but they only evaluate one aspect of assembly quality. Conversely, analyzing the coverage of pre-selected reference protein-coding genes provides essential content-based quality assessment, but the currently available pipelines for this purpose, CEGMA and BUSCO, do not have a user-friendly interface to serve as a uniform environment for assembly completeness assessment.

Results: Here, we introduce a brand-new web server, gVolante, which provides an online tool for (i) on-demand completeness assessment of sequence sets by means of the previously developed pipelines CEGMA and BUSCO and (ii) browsing pre-computed completeness scores for publicly available data in its database section. Completeness assessments performed on gVolante report scores based on not just the coverage of reference genes but also on sequence lengths (e.g. N50 scaffold length), allowing quality control in multiple aspects. Using gVolante, one can compare the quality of original assemblies between their multiple versions (obtained through program choice and parameter tweaking, for example) and evaluate them in comparison to the scores of public resources found in the database section.

Availability and implementation: gVoalte is freely available at https://gvolante.riken.jp/.

Contact: shigehiro.kuraku@riken.jp.

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Figures

Fig. 1
Fig. 1
Functions of gVolante. The web server provides two functions, ‘Analysis’ in the upper row and ‘Database’ in the lower row. Using gVolante, one can compare the quality of original assemblies and evaluate them in comparison to the scores of public resources found in the database section, for content-based decision-making for more comprehensive downstream analyses
See this image and copyright information in PMC

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