fitGCP

Fitting genome coverage distributions with mixture models

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Description

Genome coverage, the number of sequencing reads
mapped to a position in a genome, is an insightful indicator of irregularities within sequencing experiments. While the average genome coverage is frequently used within algorithms in computational
genomics, the complete information available in coverage profiles (i.e. histograms over all coverages) is currently not exploited to its full extent. Thus, biases such as fragmented or erroneous reference
genomes often remain unaccounted for. Making this information accessible can improve the quality of sequencing experiments and quantitative analyses.

fitGCP is a framework for fitting mixtures of probability distributions to genome coverage profiles. Besides commonly used distributions, fitGCP uses distributions tailored to account for
common artifacts. The mixture models are iteratively fitted based on the Expectation-Maximization algorithm.

Please find the accompanying paper here:
http://dx.doi.org/10.1093/bioinformatics/btt147

fitGCP Web Site

Categories

Bio-Informatics

License

BSD License

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Additional Project Details

Intended Audience

Education, Healthcare Industry, Science/Research

User Interface

Command-line

Programming Language

Python

Registered

2013-01-28
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