TIGRA protocols

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TIGRA specifications

Information


Unique identifier OMICS_04667
Name TIGRA
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input format BAM
Operating system Unix/Linux
Programming languages C++
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Ken Chen <>

Publication for TIGRA

TIGRA in pipeline

2016
PMCID: 4748267
PMID: 26862001
DOI: 10.1038/srep21597

[…] five steps. first, splicing breakpoints are identified by using a read-pair algorithm, or a splice mapping algorithm. then, shorts reads anchored around each breakpoint are locally constructed using tigra. this creates a set of splice junction contigs, which are supported by mapped, and one-end anchored reads. step three involves the use of blat to align junction sequences to the genome. […]


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TIGRA in publications

 (32)
PMCID: 5913189
PMID: 29692645
DOI: 10.3897/zookeys.750.23536

[…] ; hw 0.58–0.65 mm; hl 0.43–0.48 mm; hw/hl 1.35–1.4; bl 1.7–2.2 mm; fwl 1.4–2.1 mm; cl 0.8–1.0 mm; cw 0.2–0.36 mm; cl/cw2.8–4., paratype males. no males., holotype female: alajuela, san pedro de la tigra cacao, 200 m, iii–iv.1990 (r. cespedes) [uwim]. paratype female: 1♀, guanacaste, est. pitilla 9 km s santa cecilia, 700 m, v.1989 (i. gauld)., leptodrepana sohailae may be distinguished […]

PMCID: 5896245
PMID: 29634948
DOI: 10.1016/j.ccell.2018.03.013

[…] are displayed in b using the r circlize package ()., exact breakpoint types and corresponding single-base resolution were reconstructed through an in-house analysis pipeline centered around the tigra assembler (). briefly, the structural variant breakpoint predictions identified by brass were given as input to tigra. tigra was used to select structural variant-supporting reads from tumors […]

PMCID: 5880262
PMID: 29440180
DOI: 10.1101/mcs.a002444

[…] followed by manual review to differentiate somatic from germline copy-number events., putative structural variants were detected using the union of breakdancer 1.4.5 () filtered by novo-realign and tigra-sv, and squaredancer 0.1 (https://github.com/genome/genome/blob/master/lib/perl/genome/model/tools/sv/squaredancer.pl)., total rna was concurrently isolated from each fresh frozen tumor […]

PMCID: 5904369
PMID: 29674874
DOI: 10.3897/zookeys.737.20741

[…] in rotting trees, j.v. mankins (2 paratypes, uvgc); 6-10-77, l. yojoa, hond., j.v. mankins collector, dibujo e. aranda (1 paratype, inecol); francisco morazán, arriba de el rosario, fca. la tigra, 1700m, 20 vii 1991, j.c. schuster, bosque nuboso, en tronco podrido (2 males, 2 females, uvgc); rosario, san juancito mts., honduras, elev. 5120 feet, vii,[space],1930, honduras exped, o. […]

PMCID: 5832098
PMID: 29666670
DOI: 10.1155/2018/4038034

[…] of this method. they are also grateful to professors ferenc bari, ph.d., d.sc, and józsef tolnai, ph.d., for their support and for the cardiax ecg device. this project ginop-2.2.1-15-2017-00073 (tigra) was supported by the european union and cofinanced by the european regional development fund., the authors declare that there is no conflict of interest regarding the publication […]


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TIGRA institution(s)
Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA

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