Difference between revisions of "NgsCAT"
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(Created page with "Category:SoftwareCategory:Bioinformatics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|ngscat}} |{{#vardefine:url|http://www.bioinfomgp.org/ngscat}} <!--CONFIGURA...") |
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high-throughput sequencing experiments in terms of: | high-throughput sequencing experiments in terms of: | ||
| − | * Sensitivity, which assesses the quality of the coverage on target regions. | + | * Sensitivity, which assesses the quality of the coverage on target regions. It is also important to provide a means of estimating how this coverage |
| − | It is also important to provide a means of estimating how this coverage | ||
would improve by increasing sequencing depth. | would improve by increasing sequencing depth. | ||
* Specificity, which measures how much of the sequencing effort is wasted on | * Specificity, which measures how much of the sequencing effort is wasted on | ||
Revision as of 02:09, 28 January 2015
Description
ngsCAT (Next Generation Sequencing data Capture Assessment Tool) is a command-line application written in Python which facilitates a comprehensive evaluation of the performance of the capture step in targeted high-throughput sequencing experiments in terms of:
- Sensitivity, which assesses the quality of the coverage on target regions. It is also important to provide a means of estimating how this coverage
would improve by increasing sequencing depth.
- Specificity, which measures how much of the sequencing effort is wasted on
sequencing off-target bases.
- Uniformity, which assesses sequencing biases due to specific genomic
locations or nucleotide composition.
Required Modules
Serial
- ngscat
System Variables
- HPC_{{#uppercase:ngscat}}_DIR - installation directory
Citation
If you publish research that uses ngscat you have to cite it as follows:
Francisco J.López-Domingo, Javier P.Florido, Antonio Rueda, Joaquín Dopazo and Javier Santoyo-López (2014) ngsCAT: a tool to assess the efficiency of targeted enrichment sequencing, Bioinformatics, vol.30, no.12, pp.1767-1768, 2014; doi:10.1093/bioinformatics/btu108.
