RNA-Skim specifications

Information


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

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Maintainer


  • person_outline Wei Wang <>

Publication for RNA-Skim

RNA-Skim in publications

 (2)
PMCID: 5470212
PMID: 28610557
DOI: 10.1186/s12859-017-1714-9

[…] 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 […]

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

[…] 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 […]


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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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