Snakemake管线，用于生成MAG，GEM重建以及模拟微生物在实验室群落，人类肠道.rar

[](https://gitter.im/metaGEM/community) # `metaGEM` :gem: > A workflow to predict metabolic interactions within microbial communities directly from metagenomic data.  `metaGEM` integrates an array of existing bioinformatics and metabolic modeling tools using Snakemake, for the purpose of predicting metabolic interactions within bacterial communities of microbiomes. From whole metagenome shotgun datasets, metagenome assembled genomes (MAGs) are reconstructed, which are then converted into genome-scale metabolic models (GEMs) for *in silico* simulations of cross feeding interactions within sample based communities. Additional outputs include abundance estimates, taxonomic assignment, growth rate estimation, pangenome analysis, and eukaryotic MAG identification. ## :bulb: Quickstart You can start using `metaGEM` with just one line of code: ``` git clone https://github.com/franciscozorrilla/metaGEM.git && cd metaGEM && rm -r .git && bash env_setup.sh ``` Congratulations, you can now start using `metaGEM`! Please consult the [setup page](https://github.com/franciscozorrilla/metaGEM/wiki/Quickstart) in the wiki for further configuration instructions. ## :school_satchel: Tutorial `metaGEM` can even be used to explore your own gut microbiome sequencing data from at-home-test-kit services such as [unseen bio](https://unseenbio.com/). The [following tutorial](https://github.com/franciscozorrilla/unseenbio_metaGEM) showcases the `metaGEM` workflow on two unseenbio samples. ## :book: Wiki Refer to the [wiki](https://github.com/franciscozorrilla/metaGEM/wiki) for additional usage tips, frequently asked questions, and implementation details. ## :wrench: Workflow ### Core 1. Quality filter reads with [fastp](https://github.com/OpenGene/fastp) 2. Assembly with [megahit](https://github.com/voutcn/megahit) 3. Draft bin sets with [CONCOCT](https://github.com/BinPro/CONCOCT), [MaxBin2](https://sourceforge.net/projects/maxbin2/), and [MetaBAT2](https://sourceforge.net/projects/maxbin2/) 4. Refine & reassemble bins with [metaWRAP](https://github.com/bxlab/metaWRAP) 5. Taxonomic assignment with [GTDB-tk](https://github.com/Ecogenomics/GTDBTk) 6. Relative abundances with [bwa](https://github.com/lh3/bwa) and [samtools](https://github.com/samtools/samtools) 7. Reconstruct & evaluate genome-scale metabolic models with [CarveMe](https://github.com/cdanielmachado/carveme) and [memote](https://github.com/opencobra/memote) 8. Species metabolic coupling analysis with [SMETANA](https://github.com/cdanielmachado/smetana) ### Bonus 9. Growth rate estimation with [GRiD](https://github.com/ohlab/GRiD), [SMEG](https://github.com/ohlab/SMEG) or [CoPTR](https://github.com/tyjo/coptr) 10. Pangenome analysis with [roary](https://github.com/sanger-pathogens/Roary) 11. Eukaryotic draft bins with [EukRep](https://github.com/patrickwest/EukRep) and [EukCC](https://github.com/Finn-Lab/EukCC) ## :construction: Active Development If you want to see any new additional or alternative tools incorporated into the `metaGEM` workflow please raise an issue or create a pull request. Snakemake allows workflows to be very flexible, so adding new rules is as easy as filling out the following template and adding it to the Snakefile: ``` rule package-name: input: rules.rulename.output output: f'{config["path"]["root"]}/{config["folder"]["X"]}/{{IDs}}/output.file' message: """ Helpful and descriptive message detailing goal of this rule/package. """ shell: """ # Well documented command line instructions go here # Load conda environment set +u;source activate {config[envs][package]};set -u; # Run tool package-name -i {input} -o {output} """ ``` ## :paperclip: Publications The `metaGEM` workflow was used in the following publication(s): ``` Plastic-degrading potential across the global microbiome correlates with recent pollution trends Jan Zrimec, Mariia Kokina, Sara Jonasson, Francisco Zorrilla, Aleksej Zelezniak bioRxiv 2020.12.13.422558; doi: https://doi.org/10.1101/2020.12.13.422558 ``` ## :heavy_check_mark: Please cite ``` metaGEM: reconstruction of genome scale metabolic models directly from metagenomes Francisco Zorrilla, Kiran R. Patil, Aleksej Zelezniak bioRxiv 2020.12.31.424982; doi: https://doi.org/10.1101/2020.12.31.424982 ``` ## ���� Contact Please reach out with any comments, concerns, or discussions regarding `metaGEM`. * Gitter: [@metaGEM](https://gitter.im/metaGEM/community) * Twitter: [@metagenomez](https://twitter.com/metagenomez) * LinkedIn: [@fzorrilla94](https://www.linkedin.com/in/fzorrilla94/) * Email: fz274@cam.ac.uk