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PASSion | A pattern growth algorithm-based pipeline for splice junction detection in paired-end RNA-Seq data

Allows users to analyze paired-end RNA-Seq reads. PASSion provides a package able to detect known and novel junctions, as well as canonical and non-canonical ones, with single nucleotides polymorphisms (SNP) or sequencing error tolerance. The application is based on a pattern growth algorithm and includes an additional feature that permits to identify shared and sample specific splice junctions between multiple samples.

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PASSion forum

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PASSion classification

PASSion specifications

Unique identifier:
OMICS_01246
Interface:
Command line interface
Operating system:
Unix/Linux
Computer skills:
Advanced
Requirements:
GCC, SMALT, SAMtools
Software type:
Package/Module
Restrictions to use:
None
Programming languages:
C++, Perl, Shell (Bash)
Version:
1.2.0
Maintained:
No

PASSion distribution

versioning

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No versioning.

PASSion support

Maintainers

This tool is not available anymore.

Additional information

https://trac.nbic.nl/passion/wiki/Manual

Credits

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Publications

Institution(s)

Department of Molecular Epidemiology, Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands; Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands; The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Netherlands Consortium for Healthy Ageing, Leiden, The Netherlands

Funding source(s)

Supported by Netherlands Consortium for Healthy Ageing in the framework of the Netherlands Genomics Initiative/Netherlands Organization for Scientific Research (Grant no. 05060810); European Union’s Seventh Framework Programme (FP7/2007- 2011) under grant agreement (no. 259679), IDEAL; Netherlands Organization for Scientific Research VENI (Grant no. 639.021.125) (in part); European Commission 7th Framework Program Project (no. 261123), GEUVADIS (in part); and the Centre for Medical Systems Biology within the framework of the Netherlands Genomics Initiative/Netherlands Organisation for Scientific Research (in part).

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