.. This file is part of khmer, https://github.com/dib-lab/khmer/, and is Copyright (C) 2010-2015 Michigan State University Copyright (C) 2015-2016 The Regents of the University of California. It is licensed under the three-clause BSD license; see LICENSE. Contact: khmer-project@idyll.org Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * 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. * Neither the name of the Michigan State University 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. Contact: khmer-project@idyll.org ################################################################### The khmer software for advanced biological sequencing data analysis ################################################################### What is khmer? ============== The khmer software is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make *de novo* assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data. You can read more about khmer in `our software paper `__. khmer is free and open source software. **To install khmer**, you will need a Linux or Mac computer, together with Python 2.7 or Python 3.x. See :doc:`our installation docs ` for detailed instructions. **To use khmer**, you will generally need to work at the UNIX command line. See :doc:`our command line documentation `. We have **additional documentation** in several places, including `protocols for metagenome and mRNAseq assembly `__ and `recipes for several common research tasks `__. You might also be interested in :doc:`papers using or citing khmer `. **To get help**, :doc:`please follow this guide `. We welcome contributions to the khmer project! We are friendly and supportive of new contributors, and have a :doc:`code of conduct `. Please see our :doc:`docs on getting started on khmer development `. Details ======= :Authors: Michael R. Crusoe, Hussien F. Alameldin, Sherine Awad, Elmar Bucher, Adam Caldwell, Reed Cartwright, Amanda Charbonneau, Bede Constantinides, Greg Edvenson, Scott Fay, Jacob Fenton, Thomas Fenzl, Jordan Fish, Leonor Garcia-Gutierrez, Phillip Garland, Jonathan Gluck, Iván González, Sarah Guermond, Jiarong Guo, Aditi Gupta, Joshua R. Herr, Adina Howe, Alex Hyer, Andreas Härpfer, Luiz Irber, Rhys Kidd, David Lin, Justin Lippi, Tamer Mansour, Pamela McA'Nulty, Eric McDonald, Jessica Mizzi, Kevin D. Murray, Joshua R. Nahum, Kaben Nanlohy, Alexander Johan Nederbragt, Humberto Ortiz-Zuazaga, Jeramia Ory, Jason Pell, Charles Pepe-Ranney, Zachary N Russ, Erich Schwarz, Camille Scott, Josiah Seaman, Scott Sievert, Jared Simpson, Connor T. Skennerton, James Spencer, Ramakrishnan Srinivasan, Daniel Standage, James A. Stapleton, Joe Stein, Susan R Steinman, Benjamin Taylor, Will Trimble, Heather L. Wiencko, Michael Wright, Brian Wyss, Qingpeng Zhang, en zyme, C. Titus Brown :Contact: khmer-project@idyll.org :GitHub: https://github.com/dib-lab/khmer :Chat: https://gitter.im/dib-lab/khmer :License: BSD .. toctree:: :maxdepth: 1 introduction contributors citations whats-new-2.0 release-notes/index user/index dev/index roadmap LICENSE There are two mailing lists dedicated to khmer, an announcements-only list and a discussion list. To search their archives and sign-up for them, please visit the following URLs: * Discussion: http://lists.idyll.org/listinfo/khmer * Announcements: http://lists.idyll.org/listinfo/khmer-announce The archives for the khmer mailing list are available at: http://lists.idyll.org/pipermail/khmer/ khmer development was initially supported by AFRI Competitive Grant no. `2010-65205-20361 `__ from the USDA NIFA, and is now funded by the National Human Genome Research Institute of the National Institutes of Health under Award Number `R01HG007513 `__ through May 2016, both to C. Titus Brown. More recently, we have received support from the Gordon and Betty Moore Foundation under Award number GBMF4551.