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chimerascan | A tool for identifying chimeric transcription in sequencing data

Allows users to detect gene fusions in human cancers in paired-end RNA sequencing (RNA-Seq) datasets. chimerascan is an open source software, developed in Python, with the aim of providing a way of investigating various RNA-Seq data collection including those containing long paired-end reads. The application includes functionalities permitting to process ambiguously mapping reads or to identify reads spanning a fusion junction. Moreover, results can be summarized through an HTML report.

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chimerascan classification

chimerascan specifications

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

chimerascan distribution

versioning

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chimerascan support

Documentation

Maintainer

  • Christopher A. Maher <>

Additional information

https://code.google.com/archive/p/chimerascan/wikis/HowChimerascanWorks.wiki

Credits

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Publications

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

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.

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.