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        "author": "Laurent Gautier",
        "author_email": "lgautier@gmail.com",
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        "description": "# About\n\nThis code is supplementary material for the peer-reviewed publication:\n\nhttp://journals.plos.org/plosone/article?id=10.1371/journal.pone.0083784\n\n(also in [GenomeWeb](https://www.genomeweb.com/sequencing/danish-duo-introduces-microbe-identification-scheme-based-random-subset-raw-sequ))\n\n\nIt requires:\n\n- Python >= 3.3+ (currently tested with Python 3.5)\n\n- `bowtie2` in the PATH (parameter `-a`, try `--help`)\n\n- It is self-documented (try `-h` or `--help`).\n\nIt is working on FASTQ or gzipped-FASTQ files, possibly on BAM files.\n\nBe gentle and please do not hammer the server like there is no tomorrow.\n\nThe latest released versions of the package will always be on Pypi.\n\nThe terminal-based UI is looking like this:\n\n![Screenshot](screenshot.png)\n\n\nThe code is shipping with test data:\n\n- Phage Lambda DNA sequence from ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/840/245/GCF_000840245.1_ViralProj14204\n  \n\n# Installation\n\nThis installs as a regular Python package with:\n\n```bash\n\t  \npython setup.py install\n\n```\n\nIt is also available in a Docker container. The current release is version 0.3.0.\n\n```bash\n\ndocker pull lgautier/dnasnout-client:0.3.0\n\n```\n\n**Note about the docker image:** the default user is called `docker_user`,\nso the container is not running an in-container root. We are providing\na way to map the in-container user to the host user below, making\nthe execution of the software as an in-container command line\na practical option.\n\n   \n# Usage\n\n\n```bash\n\nalias dnasnout=\"python -m dnasnout_client.console\"\n\n```\n\nDeclaring an alias that runs a container from our Docker image\nthat can access the current working directory with the host's user and group ID\ncan be done with:\n\n```bash\nalias dnasnout=\"docker run \\\n                --rm -t \\\n                -v `pwd`:/shared \\\n                -u $(id -u):$(id -g) \\\n                -w /shared \\\n                lgautier/dnasnout-client:0.3.0 \\\n                python3 -m dnasnout_client.console\"\n\n```\n\nOnce the alias is declared, we can use it as a regular command:\n\n```bash\n\nwget http://tapir.cbs.dtu.dk/static/iontorrent_head400.fq\ndnasnout -i iontorrent_head400.fq -d iontorrent_test\n\n```\n\nA more difficult dataset is a metagenome sample from anterior nares in\nthe HMP Core Microbiome Sampling Protocol A (HMP-A).\n\nWe use read data available on the CloVR website: http://data.clovr.org/\n\n```bash\n\nwget http://clovr.org/files/Diginorm_sample_input.zip\nunzip Diginorm_sample_input.zip\n\ndnasnout -i Diginorm_sample_input/SRS018671.denovo_duplicates_marked.trimmed.1.fastq \\\n         -d diginorm_test \\\n\t -n 600 --bloom-filter --seed 123 --n-matches=8\n\n```\n\nUnsurprising results are:\n\n- /Staphilococcus epidermidis/ is found\n- possible human (not suprising) or mouse DNA (probable artefact from our sample strategy that alignment would clear up)\n\nUnfortunately, the human and mouse references genomes are not downloaded\n(our server is geared toward serving larger genomes) but the general idea is that one would\nfirst align the reads in such samples against the human (or mouse) genome and use dnasnout\non the unmapped reads.\n\nMore surprising results are unplaced genomic scaffold from:\n\n- /Harpegnathos saltator/\n- /Volvox carteri f. nagariensis/\n\nThese are either artefacts from our scoring, from the reference sequence (contamination\nwhen the references where sequenced).\n\n\n\nHelp is available with:\n\n```bash\n\ndnasnout --help\n\n```\n\n**note:** To update the Docker image to the latest version, `docker pull` is required each time\n(otherwise Docker will use the local image available).\n\n```bash\n\ndocker pull lgautier/dnasnout-client:latest\n\n```\n\n\n",
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        "license": "This software is available under a dual license model: the AGPLv3 or a commercial license. If you need a commercial license, contact the author.",
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