INTEGRATE-Neo statistics

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INTEGRATE-Neo specifications

Information


Unique identifier OMICS_14003
Name INTEGRATE-Neo
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data A human reference genome, gene models, gene fusions, high-throughput reference and HLA alleles sequencing reads
Input format FASTQ, FASTA, GENEPRED, BEDPE
Output data Gene fusion peptides, HLA alleles
Output format TSV, BEDPE
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, Python
Computer skills Advanced
Version 1.1.0
Stability Stable
Requirements
BWA, HLAminer, NetMHC
Maintained Yes

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Maintainer


  • person_outline Christopher A. Maher <>

Publication for INTEGRATE-Neo

INTEGRATE-Neo in publications

 (4)
PMCID: 5899330
PMID: 29653567
DOI: 10.1186/s12885-018-4325-6

[…] [–]. with little variation, these are the criteria applied by all computational tools for neoepitope prediction from tumor genomic sequencing data, including epi-seq [], epitoolkit [], pvac-seq [], integrate-neo [], tsnad [], mupexi [], and cloudneo []., our central assertion is that the immunogenicity of a neoepitope is directly related to its novelty: that is, the extent […]

PMCID: 5712389
PMID: 29234329
DOI: 10.3389/fimmu.2017.01679

[…] individual steps were recently developed. such pipelines for in silico prediction of personalized neoantigens from ngs data with different degrees of functionality include pvac-seq (), fred 2 (), integrate-neo (), and mupexi (). however, although an improvement to the use of individual steps, assembling analytical pipelines and executing workflows with a number of consecutive steps […]

PMCID: 5662567
PMID: 29084941
DOI: 10.1038/s41467-017-01178-z

[…] clustered using a drichlet process, estimating the number of mutation-defined clusters/tumor., neoepitopes resulting from gene fusions were integrated with predicted hla alleles from hlaminer by integrate-neo. for both fusion genes and mutations, netmhc 4.0 was used for neoantigen-binding prediction., sections (5 μm) of ffpe tumor tissue were stained with antibodies specific for tgfbr3 […]

PMCID: 5200911
PMID: 27793833
DOI: 10.1242/bio.021576

[…] scanning laser confocal imaging system. images were cropped, and their brightness and contrast were adjusted uniformly when necessary in adobe photoshop cs5., biolistic transformation was used to integrate neo3 (mtt1-neo) () into the micro- and macronuclear genomes in place of the conserved dead box helicase domain of lia2. a 1.5 kbp upstream region of the lia2 locus was amplified […]


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INTEGRATE-Neo institution(s)
McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MI, USA; Department of Internal Medicine, Washington University School of Medicine, St. Louis, MI, USA; Siteman Cancer Center, Washington University School of Medicine, St. Louis, MI, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MI, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MI, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MI, USA; Department of Biomedical Engineering, Washington University, St. Louis, MI, USA
INTEGRATE-Neo funding source(s)
This work was supported by an NIH NCI R21CA185983-01, NIH NCI R00CA149182 and a Prostate Cancer Foundation Young Investigator Award.

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