alu-detect specifications

Information


Unique identifier OMICS_09837
Name alu-detect
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes

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Versioning


No version available

Maintainer


  • person_outline Michael Brudno

Publication for alu-detect

alu-detect citations

 (2)
library_books

Discovery and characterization of Alu repeat sequences via precise local read assembly

2015
Nucleic Acids Res
PMCID: 4666360
PMID: 26503250
DOI: 10.1093/nar/gkv1089

[…] on the NA18506 sample resulted in 1375 putative Alu insertions having a quality score of 6 or higher. A total of 820 Alu insertions were fully assembled, of which 774 intersect with calls reported by alu-detect (out of 1727 total calls) (), again implying a FDR around 5%. […]

library_books

PopAlu: population scale detection of Alu polymorphisms

2015
PeerJ
PMCID: 4582951
PMID: 26417547
DOI: 10.7717/peerj.1269

[…] ation from sequencing data, such as SNPs and small indels, comparatively fewer methods have been developed for finding structural variation and in particular Alu polymorphisms. Notable exceptions are Alu-Detect (), VariationHunter (; ) RetroSeq (), Tangram (), and Mobster (). These methods focus mainly on the detection of Alu insertions, and generally follow a three-step analysis. First, they iden […]

alu-detect institution(s)
Department of Computer Science, University of Toronto, Toronto, ON, Canada
alu-detect funding source(s)
Canadian Institutes for Health Research (CIHR) Catalyst Grant and Ontario Research Fund (ORF) GL2 grant

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