Contra
Contra is a tool to detect copy number variation (CNV) from targeted resequencing data. It reports gains and losses in respect to a normalized depth of coverage.
Topic
Genomics;Sequencing;Oncology;DNA structural variation
Detail
Operation: Sequence analysis;Polymorphism detection;Copy number estimation;Structural variation detection
Software interface: Command-line user interface
Language: R;Python
License: GNU General Public License v3
Cost: Free
Version name: 2.0.8
Credit: Peter MacCallum Cancer Foundation Endowment Fund, the Victorian Breast Cancer Research Consortium and Australian Research Council (grant DP1096296).
Input: BAM;SAM
Output: variant call format (VCF4.0)
Contact: jason.li@petermac.org;richard.lupat@petermac.org
Collection: -
Maturity: Mature
Publications
- CONTRA: copy number analysis for targeted resequencing.
- Li J, et al. CONTRA: copy number analysis for targeted resequencing. CONTRA: copy number analysis for targeted resequencing. 2012; 28:1307-13. doi: 10.1093/bioinformatics/bts146
- https://doi.org/10.1093/bioinformatics/bts146
- PMID: 22474122
- PMC: PMC3348560
- ConTra: a promoter alignment analysis tool for identification of transcription factor binding sites across species.
- Hooghe B, et al. ConTra: a promoter alignment analysis tool for identification of transcription factor binding sites across species. ConTra: a promoter alignment analysis tool for identification of transcription factor binding sites across species. 2008; 36:W128-32. doi: 10.1093/nar/gkn195
- https://doi.org/10.1093/nar/gkn195
- PMID: 18453628
- PMC: PMC2447729
Download and documentation
Source: https://sourceforge.net/projects/contra-cnv/files/CONTRA.V2.0/
Documentation: http://contra-cnv.sourceforge.net/
Home page: http://contra-cnv.sourceforge.net/
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