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Fast genome and metagenome distance estimation using MinHash
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ondovb/Mash
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PURPOSE Mash is a fast sequence distance estimator that uses the MinHash algorithm and is designed to work with genomes and metagenomes in the form of assemblies or reads. It is implemented in C++ and is distributed with: KSeq lh3lh3.users.sourceforge.net/kseq.shtml MIT License MurmurHash3 code.google.com/p/smhasher/wiki/MurmurHash3 Public domain Open Bloom Filter https://code.google.com/p/bloom/source/browse/trunk/bloom_filter.hpp Common Public License COPYRIGHT LICENSE Copyright © 2015, Battelle National Biodefense Institute (BNBI); all rights reserved. Authored by: Brian Ondov, Todd Treangen, Sergey Koren, and Adam Phillippy This Software was prepared for the Department of Homeland Security (DHS) by the Battelle National Biodefense Institute, LLC (BNBI) as part of contract HSHQDC-07-C-00020 to manage and operate the National Biodefense Analysis and Countermeasures Center (NBACC), a Federally Funded Research and Development Center. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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Fast genome and metagenome distance estimation using MinHash
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