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IsoInfer specifications


Unique identifier OMICS_01319
Name IsoInfer
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Programming languages C, C++
Computer skills Advanced
Version 0.9.1
Stability Stable
Source code URL
Maintained Yes


No version available



  • person_outline Jianxing Feng

Publication for IsoInfer

IsoInfer citations


Accurate inference of isoforms from multiple sample RNA Seq data

BMC Genomics
PMCID: 4331715
PMID: 25708199
DOI: 10.1186/1471-2164-16-S2-S15

[…] , transcriptome assembly usually begins by mapping RNA-Seq reads to the reference genome. After that, different algorithms can be used to infer transcripts from mapped reads, including Cufflinks [,], IsoInfer [], IsoLasso [], SLIDE [], CLIIQ [], MITIE [], etc. This ab initio approach is different from the de novo approach where reference genome is not used (such as AbySS [], Trinity [], etc.), and […]


The Human Transcriptome: An Unfinished Story

PMCID: 3422666
PMID: 22916334
DOI: 10.3390/genes3030344

[…] ssemblers cluster the overlapping reads at each locus and build a connectivity graph representing all possible isoforms. Different transcriptome assembly programs, such as Cufflinks [], Scripture [], IsoInfer [], and IsoLasso [], use different criteria to parse the connectivity graph. Cufflinks uses a parsimony principle to generate the minimal number of transcripts that will explain all reads in […]

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IsoInfer institution(s)
School of Life Sciences and Technology, Tongji University, China; Department of Computer Science, University of California, Riverside, CA, USA; Tsinghua University, Beijing, China
IsoInfer funding source(s)
Supported in part by a CSC scholarship, NSF grant IIS-0711129, and NIH grants 2R01LM008991 and AI078885.

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