SVseq specifications

Information


Unique identifier OMICS_00327
Name SVseq
Software type Application/Script
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
Computer skills Advanced
Version 1
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Jin Zhang <>

Additional information


http://www.engr.uconn.edu/~jiz08001/svseq.html

Publication for SVseq

SVseq in publications

 (2)
PMCID: 4651238
PMID: 26226984
DOI: 10.1093/molbev/msv165

[…] to the predicted transcript sequences using rsem (), which were then used to find significantly differentially expressed genes using edger (). prior to differential expression analysis, we used the svseq function () of the sva package () to identify, estimate, and account for unknown sources of variation. data were filtered in two ways and the results compared. with conservative filtering, […]

PMCID: 4479793
PMID: 26161383
DOI: 10.3389/fbioe.2015.00092

[…] polymorphisms., packages implementing rp and (local) as have been also reported [novelseq (hajirasouliha et al., ), hydra (quinlan et al., )] as well as tools exploiting sr and rc/rp such as svseq, mate-clever, and prism (zhang and wu, ; jiang et al., ; marschall et al., ). prism was tested on simulated data and compared with pindel, svseq, splitread, and crest. notably, delly […]


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SVseq institution(s)
Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA
SVseq funding source(s)
Supported by National Science Foundation (grant IIS-0953563).

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