HPVDetector specifications


Unique identifier OMICS_21870
Name HPVDetector
Interface Command line interface, Graphical user interface
Restrictions to use Academic or non-commercial use
Input data A paired-end whole-exome, whole-genome or whole-transcriptome data set.
Output data A result file which enlists one or more HPV type(s) and number of HPV reads or a result file containing HPV integration loci on the human genome, annotation of HPV genes, human genes and human genome cytobands.
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Amit Dutt

Publication for HPVDetector

HPVDetector citations


Clinically actionable mutation profiles in patients with cancer identified by whole genome sequencing

PMCID: 5880257
PMID: 29610388
DOI: 10.1101/mcs.a002279

[…] a set of cancer-specific genes, as previously defined ().Presence of HPV was determined by alignment of tumor sample reads using bwa (). HPV was confirmed and the HPV-35 subtype further classified by HPVDetector (). […]


Non typhoidal Salmonella DNA traces in gallbladder cancer

PMCID: 4776363
PMID: 26941832
DOI: 10.1186/s13027-016-0057-x

[…] re found to be positive for Salmonella (data not shown). As a next step, whole exome data for these 26 samples (generated in house, manuscript in make) were analysed to detect Salmonella traces using HPVDetector pipeline, modified to include additional genome sequence of 6 common Salmonella isolates. The computational approach, in brief, subtracts all reads that align to human genome and aligns re […]

HPVDetector institution(s)
Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, India
HPVDetector funding source(s)
Supported by an Intermediate Fellowship from the Wellcome Trust/DBT India Alliance (IA/I/11/2500278); by a grant from DBT (BT/PR2372/ AGR/36/696/2011); intramural grants (IRB project 92 and 55); a senior research fellowship from ACTREC and a senior research fellowship from CSIR.

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