gdtools_vcf2gd
gdtools_vcf2gd converts Variant Call Format (VCF) files into a Galaxy-compatible GD format for downstream variant analysis within the Galaxy platform.
Key Features:
- Integration with Galaxy Platform: Processes VCF files via the Galaxy execution environment, enabling conversion to GD format and execution on the Institut Pasteur cluster.
- Web Service Compatibility: Communicates with Galaxy using the Galaxy API or the Bioblend Python library to enable execution and workflow management from external web services.
Scientific Applications:
- Variant Analysis: Converts VCF files into Galaxy-compatible formats so they can be used with Galaxy tool workflows for genomic variant analysis.
- Reproducible Research: Enables reproducible and transparent analyses by executing conversions and subsequent analyses within Galaxy histories and workflows.
Methodology:
Communication with Galaxy is performed via the Galaxy API or Bioblend and conversions are executed on the Galaxy@Pasteur server/cluster to centralize execution and optimize resource utilization at Institut Pasteur.
Topics
Collections
Details
- Maturity:
- Mature
- Tool Type:
- web application
- Operating Systems:
- Linux, Windows, Mac
- Added:
- 12/19/2016
- Last Updated:
- 6/16/2020
Operations
Publications
Mareuil F, Doppelt-Azeroual O, Ménager H. A public Galaxy platform at Pasteur used as an execution engine for web services. Unknown Journal. 2017. doi:10.7490/f1000research.1114334.1.
Barrick JE, Colburn G, Deatherage DE, Traverse CC, Strand MD, Borges JJ, Knoester DB, Reba A, Meyer AG. Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq. BMC Genomics. 2014;15(1):1039. doi:10.1186/1471-2164-15-1039. PMID:25432719. PMCID:PMC4300727.
Afgan E, Baker D, van den Beek M, Blankenberg D, Bouvier D, Čech M, Chilton J, Clements D, Coraor N, Eberhard C, Grüning B, Guerler A, Hillman-Jackson J, Von Kuster G, Rasche E, Soranzo N, Turaga N, Taylor J, Nekrutenko A, Goecks J. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Research. 2016;44(W1):W3-W10. doi:10.1093/nar/gkw343. PMID:27137889. PMCID:PMC4987906.