pileup2cov
pileup2cov converts .mpileup files into SynTView .coverage files to enable visualization and analysis of sequence coverage from next-generation sequencing (NGS) data.
Key Features:
- File Conversion: Transforms .mpileup files into SynTView .coverage files for coverage visualization and assessment of sequencing depth.
- Galaxy integration: Integrates with the Galaxy platform to execute within Galaxy workflows and leverage Galaxy execution capabilities.
Scientific Applications:
- Genomic Research: Provides SynTView-compatible coverage output to support variant calling, population genomics, and comparative genomics analyses.
- Metagenomics and Phylogenetics: Can be used in conjunction with MetaGenSense for metagenomic analysis and NGphylogeny.fr for phylogenetic studies to incorporate coverage information into broader analyses.
Methodology:
Runs within the Galaxy platform using Galaxy's execution engine (configured to run on the Institut Pasteur computing cluster) and communicates with Galaxy via the Galaxy API or the Bioblend library.
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
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.
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.