RNA-Skim specifications


Unique identifier OMICS_04642
Name RNA-Skim
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes




No version available



  • person_outline Wei Wang

Publication for RNA-Skim

RNA-Skim citations


Integration of quantitated expression estimates from polyA selected and rRNA depleted RNA seq libraries

BMC Bioinformatics
PMCID: 5470212
PMID: 28610557
DOI: 10.1186/s12859-017-1714-9

[…] their expression as a function of the reads aligned []. This alignment process is slow enough to cause an analytic bottleneck []. Alternative ‘lightweight’ algorithms (such as Sailfish [], Salmon [], RNA-skim [], RapMap [] and Kallisto []) utilise a pre-defined reference transcriptome, instead of a genome, for quantification. For instance, Kallisto builds an index of k-mers from a reference set of […]


Accelerating precision biology and medicine with computational biology and bioinformatics

Genome Biol
PMCID: 4709972
PMID: 25316263
DOI: 10.1186/s13059-014-0450-y

[…] ntigs.In RNA-Seq techniques, Zhaojun Zhang (University of Carolina at Chapel Hill, USA) indicated that the computationally expensive fragment-alignment step could be bypassed. In his algorithm named ‘RNA-Skim’, the abundance of transcripts can be estimated by means of a new concept – ‘sig-mers’ – which is defined as unique k-mers of transcript clusters. Zhang demonstrated that scanning sig-mers co […]

RNA-Skim institution(s)
Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Computer Science, University of California, Los Angeles, CA, USA
RNA-Skim funding source(s)
Supported by NIH R01HG006703, NIH P50 GM076468-08 and NSF IIS-1313606.

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