GIIRA specifications


Unique identifier OMICS_07360
Alternative name Gene Identification Incorporating RNA-Seq data and Ambiguous reads
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Stability Stable
Maintained Yes




No version available

Publication for Gene Identification Incorporating RNA-Seq data and Ambiguous reads

GIIRA citation


Dynamics in Transcriptomics: Advancements in RNA seq Time Course and Downstream Analysis

Comput Struct Biotechnol J
PMCID: 4564389
PMID: 26430493
DOI: 10.1016/j.csbj.2015.08.004

[…] ping and the quantification of reads are: ambiguous (overlapping genes), multi-alignment (repeats) and exon-junction reads, which are usually discarded at the counting step. Recent approaches such as GIIRA , ORMAN and Rcounts account for multi-mapping reads by introducing a maximum-flow optimization, minimum-weighted set cover problem of partial transcripts and weighting alignment scores, respec […]

GIIRA institution(s)
Research Group Bioinformatics (NG4), Robert Koch-Institute, Berlin, Germany

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