IDP-fusion statistics

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IDP-fusion specifications

Information


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
Requirements
Scipy, Numpy, seqmap, Bowtie, STAR, GMAP or BLAT
Maintained Yes

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Publication for IDP-fusion

IDP-fusion in publications

 (5)
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 […]

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

[…] 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 […]

PMCID: 4889949
PMID: 27105842
DOI: 10.1093/nar/gkw282

[…] () 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 […]

PMCID: 4748267
PMID: 26862001
DOI: 10.1038/srep21597

[…] then tried using the uk server (ensembldb.ensembl.org), and found that running fusionfinder from the uk server took an incomprehensible amount of time when compared to the other software packages. idp-fusion is a hybrid fusion detection software tool, designed to run for long reads (product of third generation sequencing technologies) mixed with short reads, which does not fit the purpose […]

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

[…] 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, […]


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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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