Machine Learning

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SHRiMP

Together with Stephen Rumble (with contributions from Adrian Dalca, Marc Fiume, Vlad Yanovsky, and in a collaboration with Arend Sidow and his group) we developed SHRiMP — the SHort Read Mapping Program. SHRiMP can align short reads to a reference genome quickly and accurately, while allowing for insertions/deletions. It also comes with special color-space options to handle reads made by the AB SOLiD technology. More recently Matei David, Misko Dzamba, and others have worked on the second version of SHRiMP (SHRiMP2), which significantly speeds up mapping without sacrificing sensitivity.