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Protocols

Tangram specifications

Information


Unique identifier OMICS_05785
Name Tangram
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Some reads aligned to the genome reference sequence.
Input format BAM
Operating system Unix/Linux
Programming languages C, C++
License MIT License
Computer skills Advanced
Stability Stable
Requirements
g++, zlib, pthread lib
Maintained Yes

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Documentation


Maintainer


  • person_outline Jiantao Wu

Publication for Tangram

Tangram citations

 (5)
call_split

Population and clinical genetics of human transposable elements in the (post) genomic era

2017
Mob Genet Elements
PMCID: 5305044
PMID: 28228978
DOI: 10.1080/2159256X.2017.1280116
call_split See protocol

[…] for calling TE insertions in the first phase of the 1KGP. Subsequent phases of the 1KGP included additional refinement of next-generation sequence based TE insertion calling methods resulting in the Tangram and MELT programs, for the second and third phases of the project, respectively. RetroSeq and Mobster are two of the other most widely used programs for sequence based TE insertion detection. […]

library_books

Detection of Genomic Structural Variants from Next Generation Sequencing Data

2015
Front Bioeng Biotechnol
PMCID: 4479793
PMID: 26161383
DOI: 10.3389/fbioe.2015.00092

[…] can be ascribed to RP and SR methods, “the mates of the anchoring reads are then mapped to a custom but configurable library of known active ME consensus sequences” (Thung et al., ).Among WGS tools, Tangram (Wu et al., ), a tool developed using Mosaik (Lee et al., ) alignments (though it may use alignments produced by other mappers), Next-Generation VariationHunter (Hormozdiari et al., ), Tea (Le […]

library_books

Toolbox for Mobile Element Insertion Detection on Cancer Genomes

2015
Cancer Inform
PMCID: 4338948
PMID: 25931804
DOI: 10.4137/CIN.S24657

[…] genome to date. Although effective, SPANNER was computationally expensive and not easily portable, precluding its use by scientists wishing to study MEIs in larger datasets.Recently, we developed the TANGRAM software (https://github.com/jiantao/Tangram) to overcome some of these limitations. TANGRAM is fast, accurate, and easy to use, and it is currently employed in the 1000 Genomes Project Phase- […]

library_books

PopAlu: population scale detection of Alu polymorphisms

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

[…] l 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 identify fragments (reads or read pairs) that indicat […]

library_books

Toolbox for Mobile Element Insertion Detection on Cancer Genomes

2014
Cancer Inform
PMCID: 4218655
PMID: 25452688
DOI: 10.4137/CIN.S13979

[…] genome to date. Although effective, SPANNER was computationally expensive and not easily portable, precluding its use by scientists wishing to study MEIs in larger datasets.Recently, we developed the TANGRAM software (https://github.com/jiantao/Tangram) to overcome some of these limitations. TANGRAM is fast, accurate, and easy to use, and it is currently employed in the 1000 Genomes Project Phase- […]


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Tangram institution(s)
Department of Biology, Boston College, Chestnut Hill, MA, USA; Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA; Department of Human Genetics and USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA
Tangram funding source(s)
Supported by grants R01HG004719 and U01HG006513 from the National Human Genome Research Institute and by grant RO1GM59290 from the National Institutes of Health.

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