SvABA statistics

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SvABA specifications

Information


Unique identifier OMICS_16277
Name SvABA
Alternative name Structural variation and indel Analysis By Assembly
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Rameen Beroukhim <>

Publication for Structural variation and indel Analysis By Assembly

SvABA in publication

PMCID: 5896245
PMID: 29634948
DOI: 10.1016/j.ccell.2018.03.013

[…] further validate the breakpoint junction sequences (). as an additional check, the results obtained through our tigra pipeline were also reproduced using the assembly based structural variant caller svaba ()., sv breakpoints were intersected with ensembl gene predictions. svs that were predicted within a gene footprint are annotated in . strand and frame information was used to predict […]


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SvABA institution(s)
The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Bioinformatics and Integrative Genomics, Harvard University, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Seven Bridges Genomics, Cambridge, MA, USA; Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK; The Finsen Laboratory, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark; Tri-Institutional PhD Program in Computational Biology and Medicine, New York, NY, USA; New York Genome Center, New York, NY, USA; Department of Haematology, University of Cambridge, Cambridge, UK; Department of Pathology and Cancer Center, Massachusetts General Hospital, Boston, MA, USA; Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; Department of Pathology and Laboratory Medicine, Englander Institute for Precision Medicine, Institute for Computational Biomedicine, and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
SvABA funding source(s)
Supported by The National Institutes of Health (T32 HG002295/HG/ NHGRI, U54CA143798, and R01CA188228), DFCI-Novartis Drug Discovery Program, Voices Against Brain Cancer, Pediatric Low-Grade Astrocytoma Foundation, the Broad Institute, and the Cure Starts Now Foundation.

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