Difference between revisions of "VirusSeq"
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{{Bioinformatics application | {{Bioinformatics application | ||
| − | |sw summary=We developed a new algorithmic method, VirusSeq, for detecting known viruses and their integration sites in the human genome using next-generation sequencing data. We evaluated VirusSeq on RNA-Seq data of 256 TCGA human cancer samples. Using these data, we showed that VirusSeq accurately detects the known viruses and their integration sites with high sensitivity and specificity. VirusSeq can also perform this function using whole genome sequencing data of human tissue. | + | |sw summary=We developed a new algorithmic method, VirusSeq, for detecting known viruses and their integration sites in the human genome using next-generation sequencing data. We evaluated VirusSeq on RNA-Seq data of 256 TCGA human cancer samples. Using these data, we showed that VirusSeq accurately detects the known viruses and their integration sites with high sensitivity and specificity. VirusSeq can also perform this function using whole genome sequencing data of human tissue. |
| − | + | |bio domain=Genomics, Mapping | |
| − | |bio domain= | + | |bio method=Read mapping |
| − | |bio method= | + | |bio tech=Illumina, |
| − | |bio tech=Illumina, | ||
|created by=Xiaoping Su | |created by=Xiaoping Su | ||
|created at=The University of Texas MD Anderson Cancer Center | |created at=The University of Texas MD Anderson Cancer Center | ||
|maintained=Maybe | |maintained=Maybe | ||
| − | |input format=FASTQ, | + | |input format=FASTQ, |
| − | |language=Perl, | + | |language=Perl, |
| − | |licence= | + | |licence=Unknown, |
}} | }} | ||
== Description == | == Description == | ||
Latest revision as of 20:36, 19 December 2015
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Application data |
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| Created by | Xiaoping Su |
|---|---|
| Biological application domain(s) | Genomics, Mapping |
| Principal bioinformatics method(s) | Read mapping |
| Technology | Illumina |
| Created at | The University of Texas MD Anderson Cancer Center |
| Maintained? | Maybe |
| Input format(s) | FASTQ |
| Programming language(s) | Perl |
| Licence | Unknown |
Summary: We developed a new algorithmic method, VirusSeq, for detecting known viruses and their integration sites in the human genome using next-generation sequencing data. We evaluated VirusSeq on RNA-Seq data of 256 TCGA human cancer samples. Using these data, we showed that VirusSeq accurately detects the known viruses and their integration sites with high sensitivity and specificity. VirusSeq can also perform this function using whole genome sequencing data of human tissue.
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Description
SUMMARY: We developed a new algorithmic method, VirusSeq, for detecting known viruses and their integration sites in the human genome using next-generation sequencing data. We evaluated VirusSeq on whole-transcriptome sequencing (RNA-Seq) data of 256 human cancer samples from The Cancer Genome Atlas (TCGA). Using these data, we showed that VirusSeq accurately detects the known viruses and their integration sites with high sensitivity and specificity. VirusSeq can also perform this function using wholegenome sequencing data of human tissue. AVAILABILITY: VirusSeq has been implemented in PERL and is available at http://odin.mdacc.tmc.edu/~xsu1/VirusSeq.html CONTACT: xsu1@mdanderson.org.
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