GROC-SVs statistics

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GROC-SVs specifications

Information


Unique identifier OMICS_12774
Name GROC-SVs
Alternative name Genome-wide Reconstruction of Complex Structural Variants
Software type Pipeline/Workflow
Interface Command line interface, Graphical user interface
Restrictions to use None
Input format FASTA, BED, BEDPE
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
Computer skills Advanced
Stability Stable
Requirements
idba_ud, samtools, bwa-mem
Maintained Yes

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Documentation


Maintainer


  • person_outline Arend Sidow <>

Publication for Genome-wide Reconstruction of Complex Structural Variants

GROC-SVs in publication

PMCID: 5578891
PMID: 28714986
DOI: 10.1038/nmeth.4366

[…] them, retains long-range information in short sequencing reads. such read cloud approaches represent a powerful and cost-effective alternative to single-molecule long-read sequencing. we developed groc-svs, which uses read clouds for structural variant detection and assembly, and apply it to illumina-sequenced 10× genomics sarcoma and breast cancer data sets. validation demonstrates […]


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GROC-SVs institution(s)
Genomescale Measurements Group, National Institute of Standards and Technology, Gaithersburg, MA, USA; Joint Initiative for Metrology in Biology, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Department of Computer Science, Stanford University, Stanford, CA, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
GROC-SVs funding source(s)
This work was supported by the Stanford Center for Computational, Evolutionary and Human Genomics, R01CA183904 and the BRCA Foundation.

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