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    "info": {
        "author": "Romain Guerillot, Torsten Seemann, Mark B Schultz",
        "author_email": "romain.guerillot@hotmail.fr",
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        "classifiers": [
            "Development Status :: 3 - Alpha",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+)",
            "Programming Language :: Python :: 3.5",
            "Topic :: Scientific/Engineering :: Bio-Informatics",
            "Topic :: Scientific/Engineering :: Medical Science Apps."
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        "description": "RM-seq: Resistance Mutation SEQuencing\n======================================\n\nAnalysis bioinformatic pipeline for high-throughput assessment of\nresistance mutations. RM-seq is an amplicon-based, deep-sequencing\ntechnique using single molecule barcoding. We have adapted this method\nto identify and characterise antibiotic resistance mutation.\n\nThe complete description of the RM-seq workflow is available\n`here <https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-018-0572-z>`__\n\nIs this the right tool for me?\n------------------------------\n\n1. To be able to us this pipeline you need to have sequenced amplicon\n   library with molecular barcodes.\n2. It only supports paired-end FASTQ reads (including .gz compressed\n   fastq files).\n3. It needs paired reads that are overlapping.\n4. It needs a reference fasta sequences of the sequenced gene (DNA\n   sequence).\n5. It's written in Python3 and Perl.\n\nInstallation\n------------\n\nInstall RM-seq pipeline\n~~~~~~~~~~~~~~~~~~~~~~~\n\n::\n\n    pip3 install rmseq\n\nDependencies\n~~~~~~~~~~~~\n\nRM-seq has the following package dependencies: \\* EMBOSS >= 6.6 for\n``clustalo``, ``cons``, ``getorf``, ``diffseq`` \\* clustal-omega >=\n1.2.1 \\* bwa >= 0.7.15 \\* samtools >= 1.3 \\* bedtools >= 2.26.0 \\* pear\n>= 0.9.10 \\* cd-hit >= 4.7 \\* trimmomatic >= 0.36 \\* seqtk >= 1.3-r106\n(only if you subsample reads) \\* python modules: ``plumbum``,\n``Biopython``\n\nIf you are using the `OSX Brew <http://brew.sh/>`__ or\n`LinuxBrew <http://linuxbrew.sh/>`__ packaging system:\n\n::\n\n    brew tap homebrew/science\n    brew tap tseemann/bioinformatics-linux\n    brew install parallel; parallel --citation # please write will cite\n    brew install bedtools\n    brew install EMBOSS\n    brew install clustal-omega\n    brew install bwa\n    brew install samtools\n    brew install pear\n    brew install cd-hit\n    brew install trimmomatic\n    brew install seqtk\n    pip3 install plumbum\n    pip3 install biopython\n\nQuick start\n-----------\n\nDo\n\n::\n\n    rmseq\n\nHelp\n~~~~\n\n::\n\n    usage: rmseq [-h]  ...\n\n    Run RM-seq pipeline.\n\n    optional arguments:\n      -h, --help  show this help message and exit\n\n    Commands:\n\n        run       Run the pipeline.\n        version   Print version.\n        check     Check pipeline dependencies\n        test      Run the test data set.\n\nTo check dependencies are installed\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\n::\n\n    rmseq check\n\nTo run the test dataset\n~~~~~~~~~~~~~~~~~~~~~~~\n\n::\n\n    rmseq test\n\nTo run analysis pipeline, follow the steps in\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\n::\n\n    rmseq run -h\n    usage: rmseq run [options]\n\n    Run the pipeline\n\n    positional arguments:\n       R1                    Path to read pair 1\n       R2                    Path to read pair 2\n       refnuc                Reference sequence that will be used for premapping\n                        filtering and mutation annotation (fasta).\n       outdir                Output directory.\n\n    optional arguments:\n       -h, --help            show this help message and exit\n       -d, --debug_on        Switch on debug mode.\n       -f, --force           Force overwite of existing.\n       -b BARLEN, --barlen BARLEN\n                             Length of barcode (default 16)\n       -m MINFREQ, --minfreq MINFREQ\n                             Minimum barcode frequency to keep (default 5)\n       -q BASEQUAL, --basequal BASEQUAL\n                             Minimum base quality threshold used for trimming the\n                             end of reads (trimmomatic TRAILING argument) (default\n                             30)\n       -c CPUS, --cpus CPUS  Number of CPUs to use (default 72)\n       -t TRANSLATION, --translation TRANSLATION\n                             Manually set the reading frame for translation (use 1,\n                             2 or 3 - use getorf by default)\n       -r MINSIZE, --minsize MINSIZE\n                             Minimum ORF size in bp used when annotating variants\n                             (default 200)\n       -w WSIZE, --wsize WSIZE\n                             Word-size option to pass to diffseq for comparison\n                             with reference sequence (default 5)\n       -s SUBSAMPLE, --subsample SUBSAMPLE\n                             Only examine this many reads.\n       -k, --keepfiles       Keep the intermediate files (default remove)\n       -n, --noaln           Skip reads alignment when generating consensus (to use\n                             for indel quantification only) (default align)\n\nTo check the version\n~~~~~~~~~~~~~~~~~~~~\n\n::\n\n    rmseq version\n\nOutputs\n-------\n\nRM-seq produces a tap-separated output file called amplicons.effect\nwhere each raw correspond to a consensus amplicon (a genetic variant in\nthe sequenced population):\n\n+----------------------+-------------------------+-----------------------------------------------------------------------------------------+\n| Column               | Example                 | Description                                                                             |\n+======================+=========================+=========================================================================================+\n| barcode              | GACACAACTGAGATTA        | sequence of the barcode                                                                 |\n+----------------------+-------------------------+-----------------------------------------------------------------------------------------+\n| sample               | Rifampicin1             | output folder name                                                                      |\n+----------------------+-------------------------+-----------------------------------------------------------------------------------------+\n| prot\\_mutation       | H481N                   | annotation of the amino acid change (Histidine residue 481 substituted by Asparagine)   |\n+----------------------+-------------------------+-----------------------------------------------------------------------------------------+\n| prot\\_start          | 481                     | start coordinate of the mutation                                                        |\n+----------------------+-------------------------+-----------------------------------------------------------------------------------------+\n| prot\\_end            | 481                     | end coordinate of the mutation                                                          |\n+----------------------+-------------------------+-----------------------------------------------------------------------------------------+\n| nuc\\_mutation        | C1443G                  | annotation of the nucleotide change                                                     |\n+----------------------+-------------------------+-----------------------------------------------------------------------------------------+\n| nuc\\_start           | 1443                    | start coordinate of the nucleotide change                                               |\n+----------------------+-------------------------+-----------------------------------------------------------------------------------------+\n| nuc\\_end             | 1443                    | end coordinate of the nucleotide change                                                 |\n+----------------------+-------------------------+-----------------------------------------------------------------------------------------+\n| prot                 | VRPPDKNNRFVGLYCTLV...   | protein sequence of the consensus sequence                                              |\n+----------------------+-------------------------+-----------------------------------------------------------------------------------------+\n| dna                  | GGTTAGACCACCCGATAA...   | dna sequence of the consensus sequence                                                  |\n+----------------------+-------------------------+-----------------------------------------------------------------------------------------+\n| reference\\_barcode   | CTGACACGTCCTGAAG        | barcode of the identical consesnsus amplicon used for annotation                        |\n+----------------------+-------------------------+-----------------------------------------------------------------------------------------+\n\nThe other files produced by RM-seq are:\n\n+-----------------------+---------------------------------------------------------------------------------------------------------------+\n| File name             | Description                                                                                                   |\n+=======================+===============================================================================================================+\n| amplicons.barcodes    | Table with the count of each barcode sequence                                                                 |\n+-----------------------+---------------------------------------------------------------------------------------------------------------+\n| amplicons.fna         | Multifasta file containing all the consensus nucleotide sequence (header of sequence is the barcode)          |\n+-----------------------+---------------------------------------------------------------------------------------------------------------+\n| amplicons.faa         | Multifasta file containing all the consensus protein sequence (header of sequence is the barcode)             |\n+-----------------------+---------------------------------------------------------------------------------------------------------------+\n| amplicons.fna.cdhit   | Multifasta file containing all the unique consensus nucleotide sequence (header of sequence is the barcode)   |\n+-----------------------+---------------------------------------------------------------------------------------------------------------+\n| amplicons.faa.cdhit   | Multifasta file containing all the unique consensus amino acid sequence (header of sequence is the barcode)   |\n+-----------------------+---------------------------------------------------------------------------------------------------------------+\n\nIssues\n------\n\nPlease report problems to the `Issues\nPage <https://github.com/rguerillot/RM-seq/issues>`__.\n\nAuthors\n-------\n\nRomain Guerillot (github: rguerillot) \\| Torsten Seemann (github:\ntseemann) \\| Mark B Schultz (github: schultzm)\n\nCitation\n--------\n\nIf you use this tool please cite: `Gu\u00e9rillot R et al. Comprehensive\nantibiotic-linked mutation assessment by Resistance Mutation Sequencing\n(RM-seq). 2018.\ndoi:10.1101/257915. <https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-018-0572-z>`__\n",
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        "keywords": "resistance",
        "license": "AGPL-3.0",
        "maintainer": "",
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        "name": "rmseq",
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        "summary": "RM-seq is a bioinformatics tool for for assessing resistance mutations from PE short-reads.",
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