Hello,
We've recently released a new open-source framework to facilitate the development of efficient next-gen data analyses. The framework is called Goby (we know it's just a small fish in the ocean of next-gen tools being developed lately) and described at
Goby is a framework to develop new tools, but comes with a few programs ready to use.
Released applications include:
1. Generation of wiggle plots.
2. Generation of counts over arbitrarily defined genomic annotations.
3. Group comparisons, with Fisher exact test, Chi Square test, T-test and suitable FDR corrections.
We designed Goby for speed, scalability and cross-platform support. The framework is pure Java, easy on memory and disk, and works on hardware ranging from laptop to linux clusters. We've tested it with Illumina, SOLID, Helicos and Roche 454 reads. Did I mention that we optimized algorithms and data structures for speed?
As usual, feedback, ideas, suggestions are most welcome.
Fabien
Fabien Campagne, PhD -- http://campagnelab.org
Assistant Professor, Dept. of Physiology and Biophysics
Bioinformatics Officer, Institute for Computational Biomedicine
Director, Computational Genomics Core Facility
Associate Director, Biomedical Informatics Core,
Clinical Translational Science Center
Weill Medical College of Cornell University
phone: (646)-962-5613 1305 York Avenue
fax: (646)-962-0383 Box 140
New York, NY 10021
We've recently released a new open-source framework to facilitate the development of efficient next-gen data analyses. The framework is called Goby (we know it's just a small fish in the ocean of next-gen tools being developed lately) and described at
Goby is a framework to develop new tools, but comes with a few programs ready to use.
Released applications include:
1. Generation of wiggle plots.
2. Generation of counts over arbitrarily defined genomic annotations.
3. Group comparisons, with Fisher exact test, Chi Square test, T-test and suitable FDR corrections.
We designed Goby for speed, scalability and cross-platform support. The framework is pure Java, easy on memory and disk, and works on hardware ranging from laptop to linux clusters. We've tested it with Illumina, SOLID, Helicos and Roche 454 reads. Did I mention that we optimized algorithms and data structures for speed?
As usual, feedback, ideas, suggestions are most welcome.
Fabien
Fabien Campagne, PhD -- http://campagnelab.org
Assistant Professor, Dept. of Physiology and Biophysics
Bioinformatics Officer, Institute for Computational Biomedicine
Director, Computational Genomics Core Facility
Associate Director, Biomedical Informatics Core,
Clinical Translational Science Center
Weill Medical College of Cornell University
phone: (646)-962-5613 1305 York Avenue
fax: (646)-962-0383 Box 140
New York, NY 10021
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