Difference between revisions of "ContEst"
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{{Bioinformatics application | {{Bioinformatics application | ||
|sw summary=GATK tool to estimate amount of cross-individual contaminating sequence in a dataset | |sw summary=GATK tool to estimate amount of cross-individual contaminating sequence in a dataset | ||
| − | |bio method=Sequencing | + | |bio domain=Metagenomic sequencing |
| − | |language=Java, | + | |
| − | |licence=BSD | + | |bio method=Sequencing quality control, |
| + | |interface=Command line, | ||
| + | |resource type=Command-line tool, | ||
| + | |input format=VCF, BAM | ||
| + | |language=Java, | ||
| + | |licence=BSD, | ||
}} | }} | ||
== Description == | == Description == | ||
<!-- Describe the application in the space below --> | <!-- Describe the application in the space below --> | ||
| − | Cross-contamination of samples in a large sequencing facility is inevitable, even with elaborate safeguards. ContEst estimates the degree of such contamination in a sequencing dataset. | + | Cross-contamination of samples in a large sequencing facility is inevitable, even with elaborate safeguards. ContEst estimates the degree of such contamination in a sequencing dataset, using known population allele frequencies and microarray measurements. |
Latest revision as of 14:01, 3 November 2016
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Application data |
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| Biological application domain(s) | Metagenomic sequencing |
|---|---|
| Principal bioinformatics method(s) | Sequencing quality control |
| Maintained? | Maybe |
| Input format(s) | VCF, BAM |
| Programming language(s) | Java |
| Interface type(s) | Command line |
| Resource type(s) | Command-line tool |
| Licence | BSD |
Summary: GATK tool to estimate amount of cross-individual contaminating sequence in a dataset
"Error: no local variable "counter" was set." is not a number.
Description
Cross-contamination of samples in a large sequencing facility is inevitable, even with elaborate safeguards. ContEst estimates the degree of such contamination in a sequencing dataset, using known population allele frequencies and microarray measurements.
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References
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