gVolante

About the developers

Citation

gVolante for standardizing completeness assessment of genome and transcriptome assemblies
Nishimura O, Hara Y, Kuraku S.
Bioinformatics. 2017; 33(22):3635-3637. doi: 10.1093/bioinformatics/btx445.

 
Evaluating Genome Assemblies and Gene Models Using gVolante.
Nishimura O, Hara Y, Kuraku S.
Methods Mol Biol. 2019; 1962:247-256. doi: 10.1007/978-1-4939-9173-0_15.

References

Core Vertebrate Genes (CVG)
Optimizing and benchmarking de novo transcriptome sequencing: from library preparation to assembly evaluation.
Hara Y, Tatsumi K, Yoshida M, Kajikawa E, Kiyonari H, Kuraku S.
BMC Genomics. 2015. 16: 977.

 
CEGMA and CEG
Assessing the gene space in draft genomes.
Parra G, Bradnam K, Ning Z, Keane T, Korf I.
Nucleic Acids Res. 2009. 37: 289-97.

 
BUSCO
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.
Simao FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM.
Bioinformatics. 2015. 31 :3210-2.

 
BUSCO applications from quality assessments to gene prediction and phylogenomics.
Waterhouse RM, Seppey M, Simão FA, Manni M, Ioannidis P, Klioutchnikov G, Kriventseva EV, Zdobnov EM.
Mol Biol Evol. 2017. doi: 10.1093/molbev/msx319.
 
BUSCO: Assessing Genome Assembly and Annotation Completeness.
Seppey M, Manni M, Zdobnov EM.
Methods Mol Biol. 2019; 1962:227-245. doi: 10.1007/978-1-4939-9173-0_14.

Release Notes

2021-05-05 (ver. 2.0.0)
  Major upgrade. Added BUSCO v4.1.4 and v5.1.2 with OrthoDB v10 as choices of analysis engine for completeness assessment.

 
 
2018-12-03 (ver. 1.2.1)
  Actinopterygii (ray-finned fishes) ortholog set is added as a choice for BUSCO v2/v3 analysis.

 
 
2018-07-31 (ver. 1.2.0)
  The proportions of nucleotides in the sequences longer than 1Mb and 10Mb in the entire genome
  assemblies given are computed and displayed. This allows users to assess if the major proportion of
  the given genome assembly consists of chromosome-sized sequences or not.

  The length distribution of the gaps (‘NNNNN’) is displayed in the result page of genome assessment.

  Updated the ortholog sets.

 
 
2018-01-12 (ver. 1.1.0)
  Custom parameters are available for gene prediction in CEGMA ('Max intron length' and 'Gene flanks').
  See FAQ for the details.

 
 
2017-07-12 (ver. 1.0.1)
  Protists ensembl ortholog set is added to BUSCO v2/v3 analysis.
  Bug fixes.

 
 
2017-07-06
  gVolante paper is published in Bioinformatics.
 
 
2017-04-14 (ver. 1.0.0)
  This release adds BUSCO v2 to an analysis engine for completeness assessment.

  Resource and software:
    CVG ver.10042017, CEGMA ver.2.5, BUSCO ver.1.22, BUSCO ver.2.0.1 *, GeneWise ver.2.2.3-rc7,
    Augustus ver.3.2.2, HMMER ver.3.1b2, and NCBI BLAST ver.2.2.31.
    * We have confirmed that the latest version, ‘ver.3.0.1’ yields identical results to ver.2.0.1.
 
 
2017-03-06 (ver. 0.7.2)
  Bug fixes.
 
 
2016-11-28 (ver. 0.7.1)
  This is the first public version of gVolante that contains the following resource and software:
    CVG ver.20062015, CEGMA ver.2.5, BUSCO ver.1.22, GeneWise ver.2.2.3-rc7, Augustus ver.3.2.2,
    HMMER ver.3.1b2, and NCBI BLAST ver.2.2.31.