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The goal of Bactopia\nis to process your data with a broad set of tools, so that you can get to the fun part of\nanalyses quicker!\n\nBactopia can be split into two main parts:\n[Bactopia Analysis Pipeline](https://bactopia.github.io/latest/beginners-guide/), and\n[Bactopia Tools](https://bactopia.github.io/latest/bactopia-tools/).\n\n\nBactopia Analysis Pipeline is the main *per-isolate* workflow in Bactopia. Built with\n[Nextflow](https://www.nextflow.io/), input FASTQs (local or available from SRA/ENA)\nare put through numerous analyses including: quality control, assembly, annotation,\nminmer sketch queries, sequence typing, and more.\n\n![Bactopia Overview](data/bactopia-workflow.png)\n\nBactopia Tools are a set a independent workflows for comparative analyses. The comparative analyses\nmay include summary reports, pan-genome, or phylogenetic tree construction. Using the\n[predictable output structure](https://bactopia.github.io/latest/full-guide/) of Bactopia you can\npick and choose which samples to include for processing with a Bactopia Tool.\n\nBactopia was inspired by [Staphopia](https://staphopia.github.io/), a workflow we (Tim Read and myself)\nreleased that targets *Staphylococcus aureus* genomes. Using what we learned from Staphopia and user\nfeedback, Bactopia was developed from scratch with usability, portability, and speed in mind from\nthe start.\n\n# Documentation\nDocumentation for Bactopia is available at https://bactopia.github.io/. The documentation includes\na tutorial replicating [Staphopia](https://staphopia.github.io/) and a complete overview of\nBactopia. I highly encourage you check it out!\n\n# Quick Start\n```\nmamba create -y -n bactopia -c conda-forge -c bioconda bactopia\nconda activate bactopia\nbactopia datasets\n\n# Paired-end\nbactopia --R1 R1.fastq.gz --R2 R2.fastq.gz --sample SAMPLE_NAME \\\n         --datasets datasets/ --outdir OUTDIR\n\n# Single-End\nbactopia --SE SAMPLE.fastq.gz --sample SAMPLE --datasets datasets/ --outdir OUTDIR\n\n# Multiple Samples\nbactopia prepare MY-FASTQS/ \u003e fastqs.txt\nbactopia --fastqs fastqs.txt --datasets datasets --outdir OUTDIR\n\n# Single ENA/SRA Experiment\nbactopia --accession SRX000000 --datasets datasets --outdir OUTDIR\n\n# Multiple ENA/SRA Experiments\nbactopia search \"staphylococcus aureus\" \u003e accessions.txt\nbactopia --accessions accessions.txt --dataset datasets --outdir ${OUTDIR}\n```\n\n# Installation\nBactopia has **a lot** of tools built into its workflow. As you can imagine, all these tools\nlead to numerous dependencies, and navigating dependencies can often turn into a very\nfrustrating process. With this in mind, from the onset Bactopia was developed to only\ninclude programs that are installable using [Conda](https://conda.io/en/latest/).\n\nConda is an open source package management system and environment management system that runs\non Windows, macOS and Linux. In other words, it makes it super easy to get the tools you need\ninstalled! The [official Conda documentation](https://conda.io/projects/conda/en/latest/user-guide/install/index.html)\nis a good starting point for getting started with Conda. Bactopia has been tested using the\n[Miniforge installer](https://github.com/conda-forge/miniforgel), but the\n[Anaconda installer](https://www.anaconda.com/distribution/) should work the same.\n\nOnce you have Conda all set up, you are ready to create an environment for Bactopia.\n\n```\n# Recommended\nmamba create -n bactopia -c conda-forge -c bioconda bactopia\n\n# or with standard conda\nconda create -n bactopia -c conda-forge -c bioconda bactopia\n```\n\nAfter a few minutes you will have a new conda environment suitably named *bactopia*. To\nactivate this environment, you will can use the following command:\n\n```\nconda activate bactopia\n```\n\nAnd voilà, you are all set to get started processing your data!\n\n# Please Cite Datasets and Tools\nIf you have used Bactopia in your work, please be sure to cite any datasets or tools you may\nhave used. [A list of each dataset/tool used by Bactopia has been made available](https://bactopia.github.io/latest/impact-and-outreach/acknowledgements/). \n\n*If a citation needs to be updated please let me know!*\n\n# Acknowledgements\n\nBactopia is truly a case of *\"standing upon the shoulders of giants\"*. Nearly every component\nof Bactopia was created by others and made freely available to the public.\n\nI would like to personally extend my many thanks and gratitude to the authors of these software\npackages and public datasets. If you've made it this far, I owe you a beer 🍻 (or coffee ☕!)\nif we ever encounter one another in person. Really, thank you very much!\n\n# Alternatives\nIn case Bactopia doesn't fit your needs, here are some alternatives you can checkout. I personally haven't used them, but you might find them to fit your needs! If you ran into issues using Bactopia, please feel free to [reach out](https://github.com/bactopia/bactopia/issues/new/choose)!\n\n* __[AQUAMIS](https://gitlab.com/bfr_bioinformatics/AQUAMIS)__  \nDeneke C, Brendebach H, Uelze L, Borowiak M, Malorny B, Tausch SH. *Species-Specific Quality Control, Assembly and Contamination Detection in Microbial Isolate Sequences with AQUAMIS.* __Genes__. 2021;12. doi:10.3390/genes12050644\n\n* __[ASA³P](https://github.com/oschwengers/asap)__  \nSchwengers O, Hoek A, Fritzenwanker M, Falgenhauer L, Hain T, Chakraborty T, Goesmann A. *ASA³P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates.* __PLoS Comput Biol__ 2020;16:e1007134. https://doi.org/10.1371/journal.pcbi.1007134.\n\n* __[MicroPIPE](https://github.com/BeatsonLab-MicrobialGenomics/micropipe)__  \nMurigneux V, Roberts LW, Forde BM, Phan M-D, Nhu NTK, Irwin AD, Harris PNA, Paterson DL, Schembri MA, Whiley DM, Beatson SA *MicroPIPE: validating an end-to-end workflow for high-quality complete bacterial genome construction.* __BMC Genomics__, 22(1), 474. (2021) https://doi.org/10.1186/s12864-021-07767-z\n\n* __[Nullarbor](https://github.com/tseemann/nullarbor)__  \nSeemann T, Goncalves da Silva A, Bulach DM, Schultz MB, Kwong JC, Howden BP. *Nullarbor* __Github__ https://github.com/tseemann/nullarbor \n\n* __[ProkEvo](https://github.com/npavlovikj/ProkEvo)__  \nPavlovikj N, Gomes-Neto JC, Deogun JS, Benson AK *ProkEvo: an automated, reproducible, and scalable framework for high-throughput bacterial population genomics analyses.* __PeerJ__, e11376 (2021) https://doi.org/10.7717/peerj.11376\n\n* __[Public Health Bacterial Genomics](https://github.com/theiagen/public_health_bacterial_genomics)__  \nLibuit K, Ambrosio F, Kapsak C *Public Health Bacterial Genomics* __GitHub__ https://github.com/theiagen/public_health_bacterial_genomics\n\n* __[rMAP](https://github.com/GunzIvan28/rMAP)__  \nSserwadda I, Mboowa G *rMAP: the Rapid Microbial Analysis Pipeline for ESKAPE bacterial group whole-genome sequence data.* __Microbial Genomics__, 7(6). (2021) https://doi.org/10.1099/mgen.0.000583\n\n* __[TORMES](https://github.com/nmquijada/tormes)__  \nQuijada NM, Rodríguez-Lázaro D, Eiros JM, Hernández M. *TORMES: an automated pipeline for whole bacterial genome analysis.* __Bioinformatics__ 2019;35:4207–12. https://doi.org/10.1093/bioinformatics/btz220.\n\n# Feedback\nYour feedback is very valuable! If you run into any issues using Bactopia, have questions, or have some ideas to improve Bactopia, I highly encourage you to submit it to the [Issue Tracker](https://github.com/bactopia/bactopia/issues).\n\n# License\n[MIT License](https://raw.githubusercontent.com/bactopia/bactopia/master/LICENSE)\n\n# Citation\nPetit III RA, Read TD, *Bactopia: a flexible pipeline for complete analysis of bacterial genomes.* __mSystems__. 5 (2020), https://doi.org/10.1128/mSystems.00190-20.\n\n# Author \n\n* Robert A. Petit III\n* Twitter: [@rpetit3](https://twitter.com/rpetit3)\n\n## Funding\n\nSupport for this project came (in part) from an Emory Public Health Bioinformatics Fellowship\nfunded by the [CDC Emerging Infections Program (U50CK000485) PPHF/ACA: Enhancing Epidemiology and Laboratory Capacity](https://dph.georgia.gov/EIP),\nthe [Wyoming Public Health Division](https://health.wyo.gov/publichealth/), and\nthe [Center for Applied Pathogen Epidemiology and Outbreak Control (CAPE)](https://www.linkedin.com/company/center-for-applied-pathogen-epidemiology-and-outbreak-control/).\n\n\n![Georgia Emerging Infections Program](data/gaeip-banner.png)\n![Wyoming Public Health Division](data/wyphd-banner.jpg)\n![Center for Applied Pathogen Epidemiology and Outbreak Control](data/cape-banner.png)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbactopia%2Fbactopia","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbactopia%2Fbactopia","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbactopia%2Fbactopia/lists"}