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"Programming Language :: Python :: 3.6",
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"description": "# **metapi**\n\nhello, metagenomics!\n\n## brother project\n\n* [anvio](https://github.com/merenlab/anvio)\n* [atlas](https://github.com/pnnl/atlas)\n* [sunbeam](https://github.com/sunbeam-labs/sunbeam)\n\n## motivation\n\n we all need a metagenomics pipeline for academic research.\n\n## principle\n\n* bind intelligense together\n * [github](https://github.com/search?q=metagenomics)\n * why we here?\n* do not make wheels\n * [biopython](https://github.com/biopython/biopython)\n * [bioperl](http://bioperl.org)\n * [seqan](https://github.com/seqan/seqan)\n* make full use of pipeline execution engine\n * [make](https://www.gnu.org/software/make/manual/make.html)\n * [snakemake](https://bitbucket.org/snakemake/snakemake)\n * [common workflow language](https://github.com/common-workflow-language/common-workflow-language)\n * [workflow definition language](https://software.broadinstitute.org/wdl/)\n* make full use of awesome bioinformatics tools\n * [bwa](https://github.com/lh3/bwa)\n * [samtools](https://github.com/samtools/samtools)\n * [spades](https://github.com/ablab/spades)\n * [idba](https://github.com/loneknightpy/idba)\n * [megahit](https://github.com/voutcn/megahit)\n * [metabat](https://bitbucket.org/berkeleylab/metabat)\n * [checkm](https://github.com/Ecogenomics/CheckM)\n* robust and module, extensible, update\n * one rule, one module\n * one module, one analysis\n* welcome to PR\n\n## design\n\n* execution module\n ```python\n # Snakefile\n include: \"rules/step.smk\"\n include: \"rules/simulation.smk\"\n include: \"rules/fastqc.smk\"\n include: \"rules/trimming.smk\"\n include: \"rules/rmhost.smk\"\n include: \"rules/assembly.smk\"\n include: \"rules/alignment.smk\"\n include: \"rules/binning.smk\"\n include: \"rules/cobinning.smk\"\n include: \"rules/checkm.smk\"\n include: \"rules/dereplication.smk\"\n include: \"rules/classification.smk\"\n include: \"rules/annotation.smk\"\n include: \"rules/profilling.smk\"\n ```\n\n* analysis module\n * raw data report\n * quality control\n * remove host sequences\n * assembly\n * assembly evaluation\n * binning\n * checkm\n * dereplication\n * bins profile\n * taxonomy classification\n * genome annotation\n * function annotation\n\n* test module\n * execution test\n * analysis test\n\n## install\n\n* install dependencies*\n * [snakemake](https://snakemake.readthedocs.io)\n * [pigz](https://zlib.net/pigz/)\n * [ncbi-genome-download](https://github.com/kblin/ncbi-genome-download)\n * [InSilicoSeq](https://github.com/HadrienG/InSilicoSeq)\n * [OAFilter](https://github.com/Scelta/OAFilter)\n * [sickle](https://github.com/najoshi/sickle)\n * [fastp](https://github.com/OpenGene/fastp)\n * [MultiQC](https://github.com/ewels/MultiQC)\n * [bwa](https://github.com/lh3/bwa)\n * [samtools](https://github.com/samtools/samtools)\n * [spades](https://github.com/ablab/spades)\n * [idba](https://github.com/loneknightpy/idba)\n * [megahit](https://github.com/voutcn/megahit)\n * [quast](https://sourceforge.net/projects/quast/)\n * [MetaBat](https://bitbucket.org/berkeleylab/metabat)\n * [MaxBin2](http://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html)\n * [CheckM](https://github.com/Ecogenomics/CheckM)\n * [drep](https://github.com/MrOlm/drep)\n * [prokka](https://github.com/tseemann/prokka)\n * [metaphlan2](https://bitbucket.org/biobakery/metaphlan2)\n\n ```bash\n # in python3 environment\n conda install snakemake pigz ncbi-genome-download sickle-trim fastp bwa samtools \\\n bbmap spades idba megahit maxbin2 prokka metabat2 drep quast checkm-genome\n pip install insilicoseq\n\n # in python2 envrionment\n conda install metaphlan2\n\n # database configuration\n wget https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz\n mkdir checkm_data\n cd checkm_data\n tar -xzvf ../checkm_data_2015_01_16.tar.gz\n cd ..\n ln -s checkm_data checkm_data_latest\n\n # activate python3 environment where checkm in\n checkm data setRoot checkm_data_latest\n ```\n\n* install metapi\n\n ```bash\n # recommand\n git clone https://github.com/ohmeta/metapi\n # or (maybe not latest)\n pip install metapi\n ```\n\n## example\n\n* snakemake\u4e86\u89e3\u4e00\u4e0b:)\n\n ```python\n rule bwa_mem:\n input:\n r1 = \"fastq/sample_1.fq.gz\",\n r2 = \"fastq/sample_2.fq.gz\",\n ref = \"ref/ref.index\n output:\n bam = \"sample.sort.bam\",\n stat = \"sample_flagstat.txt\"\n threads:\n 8\n shell:\n '''\n bwa mem -t {threads} {input.ref} {input.r1} {input.r2} | \\\n samtools view -@{threads} -hbS - | \\\n tee >(samtools flagstat -@{threads} - > {output.stat}) | \\\n samtools sort -@{threads} -o {output.bam} -\n '''\n ```\n\n* a simulated metagenomics data test(uncomplete)\n\n ```bash\n # in metapi/example/basic_test directory\n cd example/basic_test\n\n # look\n snakemake --dag | dot -Tsvg > dat.svg\n ```\n ![](\"examples/basic_test/dat.svg\")
\n\n ```bash\n # run on local\n snakemake\n\n # run on SGE cluster\n snakemake \\\n --jobs 80 \\\n --cluster \"qsub -S /bin/bash -cwd -q {queue} -P {project} -l vf={mem},p={cores} -binding linear:{cores}\"\n ```\n\n* a real world metagenomics data process(uncomplete)\n\n ```bash\n # in metapipe directory\n # look\n cd metapi\n snakemake --dag | dot -Tsvg > ../docs/dat.svg\n ```\n ![](\"docs/dat.svg\")
\n\n ```bash\n # run on local\n snakemake \\\n --cores 8 \\\n --snakefile metapi/Snakefile \\\n --configfile metapi/metaconfig.yaml \\\n --until all\n\n # run on SGE cluster\n snakemake \\\n --snakefile metapi/Snakefile \\\n --configfile metapi/metaconfig.yaml \\\n --cluster-config metapi/metacluster.yaml \\\n --jobs 80 \\\n --cluster \"qsub -S /bin/bash -cwd -q {cluster.queue} -P {cluster.project} -l vf={cluster.mem},p={cluster.cores} -binding linear:{cluster.cores} -o {cluster.output} -e {cluster.error}\"\n --latency-wait 360 \\\n --until all\n ```\n\n## metapi command line interface\n\n* init\n\n ```bash\n metapi --help\n\n usage: metapi [subcommand] [options]\n\n metapi, a metagenomics data process pipeline\n\n optional arguments:\n -h, --help show this help message and exit\n -v, --version print software version and exit\n\n available subcommands:\n\n init a metagenomics project initialization\n simulation a simulation on metagenomics data\n workflow a workflow on real metagenomics data\n ```\n\n\n please supply samples.tsv \n format \n | id | fq1 | fq2 | \n |----|------------|------------| \n | s1 | s1.1.fq.gz | s1.2.fq.gz | \n | s2 | s2.1.fq.gz | s2.2.fq.gz | \n\n\n ```bash\n python /path/to/metapi/metapi/metapi.py init -d . -s samples.tsv -b raw -a metaspades\n ```\n\n* list\n\n ```bash\n snakemake --snakefile /path/to/metapi/metapi/Snakefile --configfile metaconfig.yaml --list\n ``` \n\n* debug\n\n ```bash \n snakemake --snakefile /path/to/metapi/metapi/Snakefile \\\n --configfile metaconfig.yaml \\\n -p -r -n --debug-dag \\\n --until checkm_lineage_wf\n ```\n\n* simulation\n\n* workflow\n\n\n",
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