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chimerascan specifications


Unique identifier OMICS_01343
Name chimerascan
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input format FASTQ
Output format TSV/HTML
Operating system Unix/Linux
Programming languages Python
License GNU General Public License version 3.0, GNU General Public License version 2.0
Computer skills Advanced
Version 0.4.5
Stability Stable
Maintained Yes




No version available



  • person_outline Christopher A. Maher

Additional information

Publication for chimerascan

chimerascan citations


Molecular, Pathological, Radiological, and Immune Profiling of Non brainstem Pediatric High Grade Glioma from the HERBY Phase II Randomized Trial

Cancer Cell
PMCID: 5956280
PMID: 29763623
DOI: 10.1016/j.ccell.2018.04.004
call_split See protocol

[…] RNA sequences were aligned to hg19 and organized into de-novo spliced alignments using bowtie2 and TopHat version 2.1.0 ( Fusion transcripts were detected using chimerascan version 0.4.5a filtered to remove common false positives. RNASeq raw count files were used to construct an expression matrix using Roche's internal pipeline. The expression matrix was norm […]


Integrated Molecular Characterization of Gastrointestinal Stromal Tumors (GIST) Harboring the Rare D842V Mutation in PDGFRA Gene

Int J Mol Sci
PMCID: 5877593
PMID: 29510530
DOI: 10.3390/ijms19030732

[…] s was performed to examine for the presence of any chromosomal rearrangements leading to gene fusions. For this purpose, four different tools were adopted: TopHat-Fusion v.2.0.9 [], Defuse v0.6.2 [], ChimeraScan v0.4.5 [], FusionMap v2015 []. In order to increase the specificity, a predicted gene fusion was considered for further investigation if it was detected at least by two of four predictors. […]


The ten year evolutionary trajectory of a highly recurrent paediatric high grade neuroepithelial tumour with MN1:BEND2 fusion

Sci Rep
PMCID: 5773598
PMID: 29348602
DOI: 10.1038/s41598-018-19389-9

[…] M) were calculated for all known Ensembl genes in assembly v74 using bedtools ( and Cufflinks ( Putative fusions were identified using Chimerascan 0.4.5 ( Published RNAseq data was taken from Mackay et al., whilst published Affymetrix gene expression array data was taken from Sturm et al.. […]


Genomic and transcriptomic heterogeneity in metaplastic carcinomas of the breast

PMCID: 5711926
PMID: 29214215
DOI: 10.1038/s41523-017-0048-0

[…] NA-sequencing (2 × 54 bp) was performed for all 17 MBCs included in this study using the standard Illumina mRNA library protocol on a Genome Analyzer II (Illumina) as previously described. deFuse and ChimeraScan were used to identify mate-pairs supporting novel chimeric transcripts as previously described (). Candidates that resulted in open reading frames were annotated using OncoFuse. Nominated […]


The genomic landscape of pediatric myelodysplastic syndromes

Nat Commun
PMCID: 5691144
PMID: 29146900
DOI: 10.1038/s41467-017-01590-5

[…] ) and analyzed, as previously described. Structural variation detection was carried out using CICERO, a novel algorithm that uses de novo assembly to identify structural variation in RNA-seq data and Chimerascan. All identified fusions were validated by RT-PCR. Mapping statistics and coverage data are described in Supplementary Data #. Recurrent SNVs identified via WES were validated by custom amp […]


Integrated Molecular Meta Analysis of 1,000 Pediatric High Grade and Diffuse Intrinsic Pontine Glioma

Cancer Cell
PMCID: 5637314
PMID: 28966033
DOI: 10.1016/j.ccell.2017.08.017

[…] d to remove commonly multi-mapped regions to identify somatic breakpoints separated by a minimum of 10 kbp involving at least one Ensembl gene. Fusion transcripts were detected from RNAseq data using chimerascan version 0.4.5a filtered to remove common false positives. To minimize unverified false positives, reporting of nominated fusions was restricted to genes within the core functional pathways […]


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chimerascan institution(s)
Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Center for Computational Medicine and Biology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Howard Hughes Medical Institute, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
chimerascan funding source(s)
Supported by Department of Defense Breast Cancer Predoctoral Grant; Prostate Cancer Foundation Young Investigator Award and National Institutes of Health Pathway to Independence (K99 CA149182-01) Award; National Institutes of Health, Department of Defense and Early Detection Research Network.

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