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        "description": "# GraftM\nGraftM is a tool for finding genes of interest in metagenomes, metatranscriptomes, and whole genomes.\n\nUsing modular gene packages, GraftM will search the provided sequences using hmmsearch (HMMER) and place the identified sequences into a pre-constructed phylogenetic tree. The provides fast, phylogenetically informed community profiles and genome annotations. GraftM provides tools to:\n* Create and update custom gene packages to use with GraftM\n* Decorate trees, and of course..\n* Analyse sequence datasets using these GraftM packages\nHead over to the [GraftM page](http://geronimp.github.io/graftM/) for more general information.\n\n### Installation\n#### pip installation\nGraftM can be installed via pip:\n```\npip install graftm\n```\nHowever, to use all features of GraftM a few extra binary applications are required:\n* orfm v. >= 0.2.0 (https://github.com/wwood/OrfM)\n* hmmer v. >= 3.1b1 (http://hmmer.janelia.org/)\n* fxtract (https://github.com/ctSkennerton/fxtract)\n* pplacer v. >= 2.6.32 (http://matsen.fhcrc.org/pplacer/)\n* krona v. >= 2.4 (http://sourceforge.net/p/krona/home/krona/)\n* mafft v. >= 7.22 (http://mafft.cbrc.jp/)\n* diamond v. >= 0.9 (https://github.com/bbuchfink/diamond) The version of diamond used must be matched with that used to generate gpkgs, and to run the tests a specific version is required.\n\nTo create new GraftM packages, you'll also need\n* FastTreeMP (http://www.microbesonline.org/fasttree/)\n\n#### Docker images\nVersions of graftM on pip now have matching docker images as of GraftM v0.9.2. GraftM docker images are portable containers that contain the graftM code and all its python and non-python dependancies, allowing GraftM to be run on any platform with docker installed. Details on how to download and run a GraftM docker image can be found on the [graftm-docker](https://github.com/geronimp/graftM-docker) GitHub page or the [docker hub page](https://hub.docker.com/u/geronimp/).\n\n#### GNU Guix\nGraftM and all its Python and non-Python dependencies can be installed using the ACE package repository. After installing [GNU Guix](https://www.gnu.org/software/guix/)\n```\ngit clone https://github.com/Ecogenomics/ace-guix\nGUIX_PACKAGE_PATH=ace-guix guix package --install graftm\n```\n\n#### Conda\nAlthough not officially supported as an installation method, GraftM can be installed through [conda / bioconda](https://anaconda.org/bioconda/graftm).\n\n### Manual\nA [manual](https://github.com/geronimp/graftM/wiki) is available in the form of the wiki here on GitHub.\n\n### GraftM packages\nWe have a starter pack of graftM packages available including:\n\n* 16S rRNA packages\n* 15 single copy ribosomal protein marker genes\n* The methanogenesis marker mcrA\n\nAll are available at the [ACE ftp GraftM package database store](https://data.ace.uq.edu.au/public/graftm).\n\nOnce you have downloaded the package you want, just decompress it as follows:\n\n```\ntar -xvzf my.tar.gz\n```\nAnd you should be good to go!\n\n\n\n### Example: 'graft'\nWe'll use GraftM to classify a single 16S sequence from GreenGenes. Save the example file as `/tmp/eg.fasta` with the following contents:\n```\n>229854\nGAGTTTGATCCTGGCTCAGATTGAACGCTGGCGGCATGCTTAACACATGCAAGTCGAACGGCAGCATGACTTAGCTTGCT\nAAGTTGATGGCGAGTGGCGAACGGGTGAGTAACGCGTAGGAATATGCCTTAAAGAGGGGGACAACTTGGGGAAACTCAAG\nCTAATACCGCATAAACTCTTCGGAGAAAAGCTGGGGACTTTCGAGCCTGGCGCTTTAAGATTAGCCTGCGTCCGATTAGC\n```\nThen we can use GraftM's 61% OTU clustered GraftM package to detect and classify this sequence. Running graftM might look something like this:\n```\n$ graftM graft --forward /tmp/eg.fasta --graftm_package /path/to/4.01.2013_08_greengenes_61_otus.gpkg/ --output_directory eg.graftm\n\n                             GraftM 0.9.2\n\n                                GRAFT\n\n                       Joel Boyd, Ben Woodcroft\n\n                                                         __/__\n                                                  ______|\n          _- - _                         ________|      |_____/\n           - -            -             |        |____/_\n           - _     >>>>  -   >>>>   ____|\n          - _-  -         -             |      ______\n             - _                        |_____|\n           -                                  |______\n\n12/02/2015 09:52:06 AM INFO: Working on eg\n12/02/2015 09:52:06 AM INFO: 1 read(s) detected\n12/02/2015 09:52:06 AM INFO: aligning reads to reference package database\n12/02/2015 09:52:06 AM INFO: Filtered 0 short sequences from the alignment\n12/02/2015 09:52:06 AM INFO: 1 sequences remaining\n12/02/2015 09:52:06 AM INFO: Placing reads into phylogenetic tree\n12/02/2015 09:52:07 AM INFO: Placements finished\n12/02/2015 09:52:07 AM INFO: Reading classifications\n12/02/2015 09:52:07 AM INFO: Reads classified\n12/02/2015 09:52:07 AM INFO: Writing summary table\n12/02/2015 09:52:07 AM INFO: Writing biom file\n12/02/2015 09:52:07 AM INFO: Building summary krona plot\n12/02/2015 09:52:07 AM INFO: Cleaning up\n12/02/2015 09:52:07 AM INFO: Done, thanks for using graftM!\n```\nThis creates a folder `eg.graftm` which contains the results.\n\n### Example: 'create'\n\nWe encourage you to create your own GraftM packages that suit your own analysis\nneeds (e.g. new genes, more representatives, improved annotation of phylogenetic\ntrees, etc.). Here we will create a 16S package out from a highly dereplicated\ncollection provided by GreenGenes. The data here are provided in the\n[example_data/create](https://github.com/geronimp/graftM/tree/master/example_data/create)\nfolder of GraftM.\n```\n$ graftM create --output /tmp/my.gpkg --sequences 61_otus.fasta --taxonomy 61_otu_taxonomy.txt\n                         \n                             GraftM 0.9.5\n\n                            CREATE\n\n                   Joel Boyd, Ben Woodcroft\n\n                                                    /\n              >a                                   /\n              -------------                       /\n              >b                        |        |\n              --------          >>>     |  GPKG  |\n              >c                        |________|\n              ----------\n\n08/02/2016 09:18:48 AM WARNING: Deleting previous directory /tmp/my.gpkg\n08/02/2016 09:18:48 AM INFO: Building gpkg for /tmp/my.gpkg\n08/02/2016 09:18:48 AM INFO: Building seqinfo and taxonomy file from input taxonomy\n08/02/2016 09:18:48 AM INFO: Checking for duplicate sequences\n08/02/2016 09:18:48 AM INFO: Aligning sequences to create aligned FASTA file\n08/02/2016 09:19:08 AM INFO: Building HMM from alignment\n08/02/2016 09:19:09 AM INFO: Filtered 0 short sequences from the alignment\n08/02/2016 09:19:09 AM INFO: 22 sequences remaining\n08/02/2016 09:19:09 AM INFO: Checking for incorrect or fragmented reads\n08/02/2016 09:19:09 AM INFO: Removing 0 sequences from the search HMM that are redundant at the 6 rank in the taxonomy file\n08/02/2016 09:19:26 AM INFO: Building HMM from alignment\n08/02/2016 09:19:28 AM INFO: Filtered 0 short sequences from the alignment\n08/02/2016 09:19:28 AM INFO: 22 sequences remaining\n08/02/2016 09:19:28 AM WARNING: Found a non-standard character in the sequence of 4363260: e.g. 'W'\n08/02/2016 09:19:28 AM INFO: Deduplicating sequences\n08/02/2016 09:19:28 AM INFO: Removed 0 sequences as duplicates, leaving 22 non-identical sequences\n08/02/2016 09:19:28 AM INFO: Building tree\n08/02/2016 09:19:29 AM INFO: Building seqinfo and taxonomy file from input taxonomy\n08/02/2016 09:19:29 AM INFO: Creating reference package\n08/02/2016 09:19:29 AM INFO: Attempting to run taxit create with rerooting capabilities\n08/02/2016 09:19:29 AM INFO: Creating diamond database\n08/02/2016 09:19:29 AM INFO: Compiling gpkg\n08/02/2016 09:19:29 AM INFO: Cleaning up\n08/02/2016 09:19:29 AM INFO: Testing gpkg package works\n08/02/2016 09:19:37 AM INFO: Finished\n```\n\nThen, the output package `/tmp/my.gpkg` can be provided to 'graft'. There are\nmany optional arguments to 'create' which can be used to modify the process of\nmaking gpkgs.\n\nHappy grafting!\n\n### Contact\nIf you have any further comments, complaints or recomendations about GraftM, drop an email to the [SupportM](https://groups.google.com/forum/?hl=en#!forum/supportm) public help forum.\nSoftware by [Joel A. Boyd](http://ecogenomic.org/users/joel-boyd) (@geronimp) and [Ben J. Woodcroft](http://www.ecogenomic.org/users/ben-woodcroft) (@wwood) at the [Australian Centre for Ecogenomics](http://ecogenomic.org)\nReleased under GPL3 - see LICENCE.txt for licencing details\n\n### Citation\nGraftM has been published - please cite us at\n\n> **GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes**.\n> Joel A Boyd Ben J Woodcroft Gene W Tyson\n> Nucleic Acids Research, Volume 46, Issue 10, 1 June 2018, Pages e59, https://doi.org/10.1093/nar/gky174\n\n### License\nGraftM is licensed under the GNU GPL v3+. See LICENSE.txt for further details. GraftM makes use of 18S rRNA sequences sourced from the [SILVA database](https://www.arb-silva.de), which employs a dual licensing model. See SILVA.LICENCE.txt for further details.\n",
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