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        "author": "Karel Brinda, Kamil Salikhov, Simone Pignotti, Gregory Kucherov",
        "author_email": "kbrinda@hsph.harvard.edu, salikhov.kamil@gmail.com, pignottisimone@gmail.com, gregory.kucherov@univ-mlv.fr",
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        "description": "ProPhyle \u2013 accurate and resource-frugal phylogeny-based metagenomic classification\n==================================================================================\n\n.. image:: https://travis-ci.org/karel-brinda/prophyle.svg?branch=master\n        :target: https://travis-ci.org/karel-brinda/prophyle\n\n.. image:: https://codecov.io/gh/karel-brinda/prophyle/branch/master/graph/badge.svg\n        :target: https://codecov.io/gh/karel-brinda/prophyle\n\n.. image:: https://readthedocs.org/projects/prophyle/badge/?version=latest\n        :target: http://prophyle.rtfd.org\n\n.. image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square\n        :target: https://anaconda.org/bioconda/prophyle\n\n.. image:: https://badge.fury.io/py/prophyle.svg\n        :target: https://badge.fury.io/py/prophyle\n\n.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1045429.svg\n        :target: https://doi.org/10.5281/zenodo.1045429\n\n\nIntroduction\n------------\n\nProPhyle is a *k*-mer based metagenomic classifier using Burrows-Wheeler Transform.\nIts indexing strategy relies on a bottom-up propagation of *k*-mers in the tree,\nassembling contigs at each node, and matching using a standard full-text search using BWT-index.\nThe analysis of shared *k*-mers between NGS reads and the genomes in the index determines\nwhich nodes are the best candidates for their classification.\nMore information about the indexing scheme\ncan be found in our `poster <http://brinda.cz/publications/2017_prophyle_hitseq.pdf>`_.\n\nCompared to other state-of-the-arts classifiers, ProPhyle provides several unique features:\n\n* **Low memory requirements.** Compared to `Kraken <https://ccb.jhu.edu/software/kraken/>`_, ProPhyle has 9x smaller memory footprint for index construction and 5x smaller footprint for querying.\n* **Flexibility.** ProPhyle is easy to use with any user-provided phylogenetic trees and reference genomes.\n* **Standard bioinformatics formats.** `Newick/NHX <https://sites.google.com/site/cmzmasek/home/software/forester/nhx>`_ is used for representing phylogenetic trees and `SAM <https://samtools.github.io/hts-specs/SAMv1.pdf>`_ for reporting the assignments.\n* **Lossless k-mer indexing.** ProPhyle stores a list of *all* genomes containing a *k*-mer.  It can be, therefore, accurate even with trees containing similar genomes (e.g, phylogenetic trees for a single species).\n* **Deterministic behavior.** ProPhyle is a fully deterministic classifier with a mathematically well-defined behavior.\n\n\nQuick example\n-------------\n\n1. Install ProPhyle using `Bioconda <https://bioconda.github.io/>`_:\n\n.. code-block:: bash\n\n\tconda config --add channels defaults\n\tconda config --add channels conda-forge\n\tconda config --add channels bioconda\n\tconda install prophyle\n\n2. Download the `RefSeq <https://www.ncbi.nlm.nih.gov/refseq/>`_ bacterial database:\n\n.. code-block:: bash\n\n\tprophyle download bacteria\n\n3. To quickly test ProPhyle functionality, create an index for randomly sampled 10% genomes from the E.coli subtree of the NCBI taxonomy with k-mer size 31: ::\n\n.. code-block:: bash\n\n\tprophyle index -s 0.1 ~/prophyle/bacteria.nw@561 _index_ecoli\n\n4. Classify your reads:\n\n.. code-block:: bash\n\n        prophyle classify _index_ecoli reads.fq > result.sam\n\n\nDocumentation\n-------------\n\nSee `ProPhyle Documentation <http://prophyle.readthedocs.io/>`_.\n\n\n\nAlgorithm description\n---------------------\n\nB\u0159inda K, Salikhov K, Pignotti S, and Kucherov G.\n**ProPhyle: a phylogeny-based metagenomic classifier using the Burrows-Wheeler Transform.**\nPoster at HiTSeq 2017. |hitseq2017|\n\nB\u0159inda K.\n**Novel computational techniques for mapping and classifying Next-Generation Sequencing data.**\nPhD Thesis, Universit\u00e9 Paris-Est, 2016. |karel_phd|\n\n.. |karel_phd| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1045317.svg\n\t   :target: https://doi.org/10.5281/zenodo.1045317\n\n.. |hitseq2017| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1045427.svg\n\t\t:target: https://doi.org/10.5281/zenodo.1045427\n\n\nIssues\n------\n\nPlease use `Github issues <https://github.com/karel-brinda/prophyle/issues>`_.\n\n\nChangelog\n---------\n\nSee `Releases <https://github.com/karel-brinda/prophyle/releases>`_.\n\n\nLicence\n-------\n\n`MIT <https://github.com/karel-brinda/prophyle/blob/master/LICENSE.txt>`_\n\n\nAuthors\n-------\n\n`Karel Brinda <http://brinda.cz>`_ <kbrinda@hsph.harvard.edu>\n\nKamil Salikhov <kamil.salikhov@univ-mlv.fr>\n\nSimone Pignotti <pignottisimone@gmail.com>\n\n`Gregory Kucherov <http://www-igm.univ-mlv.fr/~koutcher/>`_ <gregory.kucherov@univ-mlv.fr>\n\n",
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