SpliceGrapher specifications

Information


Unique identifier OMICS_01266
Name SpliceGrapher
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages Python
Computer skills Advanced
Version 0.2.6
Stability Stable
Requirements matplotlib, PyML
Maintained Yes

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Maintainers


  • person_outline Asa Ben-Hur <>
  • person_outline Mark Rogers <>

SpliceGrapher article

SpliceGrapher citations

 (2)
2018
PMCID: 5864913

[…] approach of graph representation of splicing variants was employed33. graphs include putative exons to use for comparing and extracting as. various tools use different methods to build splicegraphs. splicegrapher32 as a python-based scripting tool constructs the splicegraph by summarizing short reads aligned to a reference genome. spladder34 integrates annotation information and rna-seq data […]

2017
PMCID: 5952954

[…] any errors; this gives a scale on how much the difficulty lies in the erroneous reads and how much in the spliced alignment problem., for creating the splicing graphs, we used the software tool splicegrapher (version 0.2.4) [10]. as splicegrapher requires being given a gene model in advance, we gave it the annotated transcripts used for the simulation. in addition to the gene model, […]

SpliceGrapher institution(s)
Department of Computer Science, Colorado State University, Fort Collins, CO, USA; Department of Biology and Program in Molecular Plant Biology, Colorado State University, Fort Collins, CO, USA; Department of Statistics, Colorado State University, Fort Collins, CO, USA
SpliceGrapher funding source(s)
Supported by NSF ABI grant 0743097.

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