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Our laboratory has developed a suite of a software for the new sequencing technologies from 454 Life Sciences, Illumina, and Applied Biosystems. If you are interested in using them, please email one of the authors for access.

[edit] Base-calling

We developed PyroBayes, a novel base calling application for pyrosequences from 454 Life Sciences. The quality values produced by PyroBayes more precisely describe the accuracy of the individual bases in 454 reads. PyroBayes

[edit] Read Alignment and Assembly

MOSAIK is an efficient, reference-guided next-generation read alignment and assembly program. MOSAIK produces gapped alignments perfect for small INDEL discovery and miRNA analysis assays.

[edit] Polymorphism Discovery

We have released a completely rewritten (in C++) version of PolyBayes which is capable of efficiently screening for single-nucleotide and insertion-deletion polymorphisms among millions of reads from the new technologies. It is now capable of accurate polymorphism discovery on entire chromosomes and genomes. PolyBayes

[edit] Assembly Viewing and Annotation

Gambit is a new cross-platform GUI (graphical user interface) application for sequence visualization and analysis.

Note: EagleView should be considered deprecated and is no longer supported.