SV-STAT specifications

Unique identifier:
OMICS_13029
Software type:
Package/Module
Restrictions to use:
None
Programming languages:
Perl, Python, Shell (Bash)
Computer skills:
Advanced
Requirements:
Dbfasta, BWA, Picard, Samtools, BioPerl, Bedtools
Maintained:
No
Name:
Structural Variation detection by STAck and Tail
Interface:
Command line interface
Operating system:
Unix/Linux
License:
GNU General Public License version 3.0
Source code URL:
https://gitorious.org/svstat/svstat?p=svstat:svstat.git

versioning

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No versioning.

SV-STAT support

Maintainer

This tool is not available anymore.

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Credits

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Publications

Institution(s)

Structural and Computational Biology and Molecular Biophysics (SCBMB) Program, Baylor College of Medicine, Houston, TX, USA; Texas Children’s Cancer Center, Baylor College of Medicine, Houston, TX, USA; W. M. Keck Center for Interdisciplinary Bioscience Training, Houston, TX, USA; Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA

Funding source(s)

This work was supported by the following grants from the NIH: National Institute of General Medical Sciences (K12 GM084897), and a training fellowship from the Keck Center for Interdisciplinary Bioscience Training of the Gulf Coast Consortia (T15 LM007093).

User review

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2 user reviews

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2 user reviews

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Ray Cui's avatar image Ray Cui's country flag

Ray Cui

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Hello. We have 250x2 PE reads of the insert size ~400bp, and also mate pair libraries of 3kb, 7kb and 10kb inserts. Is it possible to use all of these reads jointly for detecting variations? I am mainly using this to perform a final polishing of our de novo genome assembly (from the same data).

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Caleb Davis

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SV-STAT detects genomic rearrangements from NGS data with high accuracy and is complementary to existing tools. It is easy to use and has minimal dependencies.

I am the author of this tool. Please do not hesitate to contact me with any questions.

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