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Easy-to-use and powerful homomorphic encryption library
Microsoft SEAL is an open-source homomorphic encryption library that allows computations to be performed directly on encrypted data, with no need for any decryption. Developed by the Cryptography and Privacy Research group at Microsoft, it enables software engineers to build end-to-end encrypted data storage and computation services that never have to procure the customer's key.
...The command line tools of Hadoop-BAM should be understandable to all users, but they are limited in scope.
See the SeqPig project for a higher-level interface to the file formats supported by Hadoop-BAM: http://seqpig.sourceforge.net
See Seal for Hadoop-based read alignment tools, Seal: http://biodoop-seal.sourceforge.net