clc_extract_consensus
clc_extract_consensus extracts consensus sequences from cas files produced by reference assembly programs to generate consensus genomes from mapped reads for genomic analyses.
Key Features:
- cas file input: Operates on cas files generated by reference assembly programs that contain mapped read information.
- Consensus generation: Extracts consensus sequences from mapped reads contained in the input cas files.
- Galaxy integration and APIs: Integrates with the Galaxy platform and uses the Galaxy API or Bioblend library to communicate with web services and run within Galaxy workflows on the Institut Pasteur cluster.
Scientific Applications:
- Consensus Sequence Extraction: Used in genomic research to derive consensus sequences from mapped reads, supporting detection of genetic variation and assembly of reference genomes.
- Metagenomic Analysis: Supports metagenomic data analysis workflows and contributes to projects such as MetaGenSense.
Methodology:
Processes cas files produced during the reference assembly phase to extract consensus sequences from mapped read information and executes within Galaxy via the Galaxy API or Bioblend on the Institut Pasteur cluster.
Topics
Collections
Details
- Maturity:
- Mature
- Tool Type:
- web application
- Operating Systems:
- Linux, Windows, Mac
- Added:
- 12/19/2016
- Last Updated:
- 6/16/2020
Operations
Data Inputs & Outputs
Formatting
Outputs
Publications
Kumar S, Blaxter ML. Comparing de novo assemblers for 454 transcriptome data. BMC Genomics. 2010;11(1). doi:10.1186/1471-2164-11-571. PMID:20950480. PMCID:PMC3091720.
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.