SpliceGrapher protocols

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

Versioning


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Maintainers


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

Publication for SpliceGrapher

SpliceGrapher IN pipelines

 (4)
2017
PMCID: 5550469
PMID: 28794490
DOI: 10.1038/s41598-017-08138-z

[…] –allow-close-indels 2. the sequences with multiple and chimeric alignments were excluded from the following analyses. among raw unique alignments, we first filtered out false splice junctions using splicegrapher v0.2.413, in which the models of splice sites were designed as donors of gt, gc or at, and acceptor of ag or ac, respectively. the filtered alignments were clustered into independent […]

2017
PMCID: 5952954
PMID: 28069635
DOI: 10.1093/bib/bbw137

[…] 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, […]

2017
PMCID: 5952954
PMID: 28069635
DOI: 10.1093/bib/bbw137

[…] 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 takes as an input a sam format […]

2017
PMCID: 5952954
PMID: 28069635
DOI: 10.1093/bib/bbw137

[…] 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 takes as an input a sam format alignment file. for the alignment of the reads, we used gmap (version 2014-10-22) [7]., for post-processing of the splicing graph, we used an in-house […]

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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