BAMSurgeon specifications


Unique identifier OMICS_06796
Name BAMSurgeon
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data An indexed reference genome, a pre-existing file and a list of intervals along with the SV type and parameters.
Input format PY+BAM
Biological technology Illumina
Operating system Unix/Linux
Programming languages Python, Shell (Bash)
License MIT License
Computer skills Advanced
Version 1.0.0
Stability Stable
Requirements samtools/wgsim/tabix, pysam, bwa, velvet, exonerate, picard
Maintained Yes



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  • person_outline Paul┬áBoutros <>
  • person_outline Adam Ewing <>

Publications for BAMSurgeon

BAMSurgeon institution(s)
Ontario Institute for Cancer Research; Toronto, ON, Canada; Department of Biomolecular Engineering; University of California, Santa Cruz; Santa Cruz, CA, USA; Mater Research Institute; University of Queensland; Woolloongabba, QLD, Australia; Computational Biology Program; Oregon Health & Science University; Portland, OR, USA; Sage Bionetworks; Seattle, WA, USA; Department of Bioinformatics and Computational Biology; University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Genetics; University of Alabama at Birmingham; Birmingham, AL, USA; Informatics Institute; University of Alabama at Birmingham; Birmingham, AL, USA; IBM Computational Biology Center; T.J.Watson Research Center; Yorktown Heights, NY, USA; Department of Medical Biophysics; University of Toronto; Toronto, ON, Canada; Department of Pharmacology & Toxicology; University of Toronto; Toronto, ON, Canada
BAMSurgeon funding source(s)
Supported by the Ontario Institute for Cancer Research through funding provided by the Government of Ontario, Prostate Cancer Canada, the Movember Foundation - Grant #RS2014-, Movember funds through Prostate Cancer, Genome Canada through a Large-Scale Applied Project contract, the Discovery Frontiers: Advancing Big Data Science in Genomics Research program, which is jointly funded by the Natural Sciences and Engineering Research Council (NSERC) of Canada, the Canadian Institutes of Health Research (CIHR), Genome Canada, and the Canada Foundation for Innovation (CFI), a Terry Fox Research Institute New Investigator Award and a CIHR New Investigator Award, a CIHR Computational Biology Undergraduate Summer Student Health Research Award, an Australian Research Council Discovery Early Career Researcher Award DE150101117, the Mater Foundation and National Institutes of Health (NIH) grants: R01-CA180778 and U24-CA143858.

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