From The MarthLab
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
Traditional sequencing assembly viewing applications are ill-suited to efficient viewing, zooming and panning of large assemblies from the new sequencing technologies. We developed EagleView to provide a compact view of such large assemblies. EagleView also allows users to zoom in and out and to pan across assemblies. Importantly, EagleView allows users to add custom annotation tracks (similar to those in genome browsers) to facilitate hypothesis development. EagleView
