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TIGAR specifications

Information


Unique identifier OMICS_01294
Name TIGAR
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

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Documentation


Publication for TIGAR

TIGAR citations

 (3)
library_books

Improved data driven likelihood factorizations for transcript abundance estimation

2017
Bioinformatics
PMCID: 5870700
PMID: 28881996
DOI: 10.1093/bioinformatics/btx262

[…] abundances that would be most likely given the observed data (i.e. the alignments of the sequenced fragments to the underlying genome or transcriptome). bayesian methodologies such as bitseq () and tigar () were also developed and adopt different inferential approaches varying from fully bayesian approaches like collapsed gibbs sampling () to approximate inference approaches like variational […]

library_books

Bayesian identification of bacterial strains from sequencing data

2016
Microb Genom
PMCID: 5320594
PMID: 28348870
DOI: 10.1099/mgen.0.000075

[…] the probability of a read originating from a given reference sequence. there exist a number of methods solving the same problem there including rsem (; ), cufflinks (), miso (), bitseq (; ), tigar (, ), express (), sailfish () and many others. these are all based on different inference methods applied to the same probabilistic model first proposed in (). this is also essentially […]

library_books

Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA seq data

2015
Genome Biol
PMCID: 4511015
PMID: 26201343
DOI: 10.1186/s13059-015-0702-5

[…] option (16 cores; fig. ) is used. in particular, the times required to process the alignments of 100 million in silico-generated reads range between approximately 7 min (isoem) and more than 1 week (tigar2) when a single processor is used, and between about 5 min (isoem) and 8 h (rsem) when 16 cores are available for the tools that support multi-threading (tigar2 does not). with the exception […]


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TIGAR institution(s)
Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Aoba-ku, Sendai, Miyagi, Japan

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