IDP-fusion statistics

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Citations per year

Number of citations per year for the bioinformatics software tool IDP-fusion

Tool usage distribution map

This map represents all the scientific publications referring to IDP-fusion per scientific context
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IDP-fusion specifications


Unique identifier OMICS_08780
Name IDP-fusion
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
License Apache License version 2.0
Computer skills Advanced
Stability Stable
Scipy, Numpy, seqmap, Bowtie, STAR, GMAP or BLAT
Maintained Yes


No version available


Publication for IDP-fusion

IDP-fusion citations


Gaining comprehensive biological insight into the transcriptome by performing a broad spectrum RNA seq analysis

Nat Commun
PMCID: 5498581
PMID: 28680106
DOI: 10.1038/s41467-017-00050-4

[…] Several tools have been proposed to identify fusion from transcriptomic data such as JAFFA, STAR-Fusion, TopHat-Fusion, FusionCatcher, and SOAPfuse. In addition to these short-read-based techniques, IDP-fusion, and Iso-Seq methods can analyse long-read RNA-seq data to identify fused genes.Here we assessed these approaches in detecting the 71 validated gene fusions in the MCF-7 breast cancer cell- […]


Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis

PMCID: 5553090
PMID: 28868132
DOI: 10.5256/f1000research.11392.r19894

[…] dies using PacBio or ONT alone, Hybrid-Seq can reduce the requirement of data size and improve the output, especially for transcriptome-wide studies. For example, a series of Hybrid-Seq methods (IDP, IDP-fusion, IDP-ASE) have been developed to improve the transcriptome studies to isoform levels (e.g., gene isoform reconstruction, fusion genes and allele phasing) with higher sensitivity and accurac […]


IDP ASE: haplotyping and quantifying allele specific expression at the gene and gene isoform level by hybrid sequencing

Nucleic Acids Res
PMCID: 5952581
PMID: 27899656
DOI: 10.1093/nar/gkw1076

[…] TGS-only analysis and can improve the overall performance and resolution of the output data. In particular, a series of bioinformatics tools for Hybrid-Seq transcriptome data, including LSC, IDP and IDP-fusion, have been demonstrated to elucidate transcriptomes at the gene isoform level with high precision and sensitivity (,–).Here, we present a new method (termed IDP-ASE, […]


Discovering and understanding oncogenic gene fusions through data intensive computational approaches

Nucleic Acids Res
PMCID: 4889949
PMID: 27105842
DOI: 10.1093/nar/gkw282

[…] r () and CREST (), can call gene fusions in addition to other structural rearrangements. In the last 2 years, several additional fusion mapping tools have been released—FusionMetaCaller (), JAFFA (), IDP-fusion (), TRUP (), FusionCatcher and PRADA (). A number of supporting tools, such as the Bioconductor package Chimera (), offer utilities for organizing, analyzing and validating gene fusion list […]


PacBio Sequencing and Its Applications

PMCID: 4678779
PMID: 26542840
DOI: 10.1016/j.gpb.2015.08.002

[…] itate the development of models of differentiation and cell commitment within the developing embryo and a better understanding of the molecular mechanisms involved in the maintenance of pluripotency. IDP-fusion has also been recently released for the identification of fusion genes, fusion sites, and fusion gene isoforms from cancer transcriptomes . In the human MCF7 breast cancer cell line, IDP-fu […]

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IDP-fusion institution(s)
Department of Internal Medicine, University of Iowa, Iowa City, IA, USA
IDP-fusion funding source(s)
The institutional fund of the Department of Internal Medicine, University of Iowa; National Institutes of Health [RO1GM109836, RO1HG007834]

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