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and Phage Identification"],"sub_categories":["Metagenome Analysis"],"readme":"![](hecatombLogo.png)\n\n[![](https://img.shields.io/static/v1?label=CLI\u0026message=Snaketool\u0026color=blueviolet)](https://github.com/beardymcjohnface/Snaketool)\n![Anaconda-Server Badge](https://anaconda.org/bioconda/hecatomb/badges/license.svg)\n![Anaconda-Server Badge](https://anaconda.org/bioconda/hecatomb/badges/latest_release_date.svg)\n[![Documentation Status](https://readthedocs.org/projects/hecatomb/badge/?version=latest\u0026style=flat-square)](https://hecatomb.readthedocs.io/en/latest/?badge=latest)\n[![install with bioconda](https://img.shields.io/badge/Install%20with-conda-brightgreen.svg?style=flat-square)](http://bioconda.github.io/recipes/hecatomb/README.html)\n![](https://img.shields.io/conda/dn/bioconda/hecatomb?label=Conda%20downloads\u0026style=flat-square)\n[![install with PyPI](https://img.shields.io/badge/Install%20with-PyPI-brightgreen.svg?style=flat-square)](https://pypi.org/project/hecatomb/)\n[![Unit tests](https://github.com/shandley/hecatomb/actions/workflows/unit-tests.yaml/badge.svg)](https://github.com/shandley/hecatomb/actions/workflows/unit-tests.yaml)\n[![Env builds](https://github.com/shandley/hecatomb/actions/workflows/build-hecatomb-envs.yaml/badge.svg)](https://github.com/shandley/hecatomb/actions/workflows/build-hecatomb-envs.yaml)\n\n---\n\nA [hecatomb](https://en.wiktionary.org/wiki/hecatomb) is a great sacrifice or an extensive loss. \nHeactomb the software empowers an analyst to make data driven decisions to *'sacrifice'* false-positive viral reads from \nmetagenomes to enrich for true-positive viral reads. \nThis process frequently results in a great loss of suspected viral sequences / contigs.\n\n## Contents\n\n- [Documentation](#documentation)\n- [Citation](#citation)\n- [Quick Start Guide](#quick-start-guide)\n- [Inputs](#inputs)\n- [Dependencies](#dependencies)\n- [Links](#links)\n\n## Documentation\n\n[Complete documentation is hosted at Read the Docs](https://hecatomb.readthedocs.io)\n\n## Citation\n\n__Hecatomb: an integrated software platform for viral metagenomics__,\n_Michael J Roach, Sarah J Beecroft, Kathie A Mihindukulasuriya, Leran Wang, Anne Paredes, Luis Alberto Chica Cárdenas, Kara Henry-Cocks, Lais Farias Oliveira Lima, Elizabeth A Dinsdale, Robert A Edwards, Scott A Handley_,\nGigaScience, Volume 13, 2024, giae020, [https://doi.org/10.1093/gigascience/giae020](https://doi.org/10.1093/gigascience/giae020)\n\n## Quick start guide\n\n### Install Hecatomb\n\n__option 1: PIP__\n\n```bash\n# Optional: create a virtual with conda or venv\nconda create -n hecatomb python=3.10\n\n# activate\nconda activte hecatomb\n\n# Install\npip install hecatomb\n```\n\n__option 2: Conda__\n\n```bash\n# Create the conda env and install hecatomb in one step\nconda create -n hecatomb -c conda-forge -c bioconda hecatomb\n\n# activate\nconda activate hecatomb\n```\n\n__Check installation__\n\n```bash\nhecatomb --help\n```\n\n### Install databases and envs\n\n__Download the databases__\n\n```bash\n# 8 threads = 8 downloads at a time\nhecatomb install --threads 8\n```\n\n__Optional: prebuild envs__\n\nThese are automatically built when running hecatomb, but manually pre-building is useful if your cluster nodes are isolated from the internet.\n\n```shell\nhecatomb test build_envs\n```\n\n### Run test dataset\n\n```bash\n# locally: using 32 threads and 64 GB RAM by default\nhecatomb test --threads 32\n\n# HPC: using a profile named 'slurm'\nhecatomb test --profile slurm\n```\n\n### Snakemake profiles (for running on HPCs)\n\nHecatomb is powered by [Snakemake](https://snakemake.readthedocs.io/en/stable/#) and greatly benefits from the use of \nSnakemake profiles for HPC Clusters.\n[More information and example for setting up Snakemake profiles for Hecatomb in the documentation](https://hecatomb.readthedocs.io/en/latest/profiles/).\n\n__NOTE: Hecatomb currently uses Snakemake version 7. \nThe recent version 8 for Snakemake has some breaking changes, including some changes to the command line interface for cluster execution.\nAny new Snakemake v8 profiles might not work with Hecatomb.\nPlease open an issue if you need help setting up a profile.__\n\n## Inputs\n\n### Parsing samples with `--reads`\n\nYou can pass either a directory of reads or a TSV file to `--reads`. \nNote that Hecatomb expects paired read file names to include common R1/R2 tags. \n - __Directory:__ Hecatomb will infer sample names and various R1/2 tag combinations from the filenames.\n - __TSV file:__ Hecatomb expects 2 or 3 columns, with column 1 being the sample name and columns 2 and 3 the reads files.\n\n[More information and examples are available here](https://gist.github.com/beardymcjohnface/bb161ba04ae1042299f48a4849e917c8#file-readme-md)\n\n### Lonread support `--longreads`\n\nPass the `--longreads` argument to tell Hecatomb that you are using longreads.\n\n### Library preprocessing with `--trim`\n\nHecatomb uses [Trimnami](https://github.com/beardymcjohnface/Trimnami) for read trimming which supports many different\ntrimming methods. Current options are `fastp` (default), `prinseq`, `roundAB`, `filtlong` (for longreads), \n`cutadapt` (FASTA input), and `notrim` (skip trimming). See Trimnami's documentation for more information.\n\n### Configuration\n\nYou can configure advanced parameters for Hecatomb.\nCopy the default config: `hecatomb config`.\nEdit the config file in your favourite text editor: `nano hecatomb.out/hecatomb.config.yaml`.\n\n## Dependencies\n\nThe only dependency you need to get up and running with Hecatomb is [conda](https://docs.conda.io/en/latest/) or \nthe python package manager [pip](https://pypi.org/project/pip/).\nHecatomb relies on [conda](https://docs.conda.io/en/latest/) to ensure portability and ease of installation of its dependencies.\nAll of Hecatomb's dependencies are installed during installation or runtime, so you don't have to worry about a thing!\n\n## Links\n\n[Hecatomb @ PyPI](https://pypi.org/project/hecatomb/)\n\n[Hecatomb @ bioconda](https://bioconda.github.io/recipes/hecatomb/README.html)\n\n[Hecatomb @ bio.tools](https://bio.tools/hecatomb)\n\n[Hecatomb @ WorkflowHub](https://workflowhub.eu/workflows/235)\n\n[Hecatomb RRID:SCR_025002](https://scicrunch.org/resources/data/record/nlx_144509-1/SCR_025002/resolver)\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fshandley%2Fhecatomb","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fshandley%2Fhecatomb","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fshandley%2Fhecatomb/lists"}