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Rolexa | Probabilistic base calling of Solexa sequencing data

Allows fast and accurate base calling of Solexa's fluorescence intensity files and the production of informative diagnostic plots. Rolexa is based on a base calling algorithm using model-based clustering and probability theory to identify ambiguous bases and code them with IUPAC symbols. It provides probabilistic base calling, quality checks and diagnostic plots for Solexa sequencing data. We also select optimal sub-tags using a score based on information content to remove uncertain bases towards the ends of the reads. This method improves genome coverage and number of usable tags as compared with Solexa's data processing pipeline by an average of 15%.

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Rolexa forum

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Rolexa classification

Rolexa specifications

Unique identifier:
OMICS_01156
Interface:
Command line interface
Input format:
INT or CIF
Operating system:
Unix/Linux, Mac OS, Windows
License:
GNU General Public License version 2.0
Version:
1.27.0
Requirements:
graphics, grDevices, methods, ShortRead
Software type:
Package/Module
Restrictions to use:
None
Biological technology:
Illumina
Programming languages:
R
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes

Rolexa distribution

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Rolexa support

Maintainer

  • Jacques Rougemont <>

Credits

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Publications

Institution(s)

School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland; Ludwig Institute for Cancer Research (LICR), Université de Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), Université de Lausanne, Lausanne, Switzerland; Vital-IT, Université de Lausanne, Lausanne, Switzerland; Fasteris SA, Plan-les-Ouates, Switzerland

Funding source(s)

The Swiss National Science Foundation grant no 3100A0-113617

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