[](https://github.com/beardymcjohnface/Snaketool)
[](https://hecatomb.readthedocs.io/en/latest/?badge=latest)
[](http://bioconda.github.io/recipes/hecatomb/README.html)
[](https://pypi.org/project/hecatomb/)
[](https://github.com/shandley/hecatomb/actions/workflows/unit-tests.yaml)
[](https://github.com/shandley/hecatomb/actions/workflows/build-hecatomb-envs.yaml)
---
A [hecatomb](https://en.wiktionary.org/wiki/hecatomb) is a great sacrifice or an extensive loss.
Heactomb the software empowers an analyst to make data driven decisions to *'sacrifice'* false-positive viral reads from
metagenomes to enrich for true-positive viral reads.
This process frequently results in a great loss of suspected viral sequences / contigs.
## Contents
- [Documentation](#documentation)
- [Citation](#citation)
- [Quick Start Guide](#quick-start-guide)
- [Inputs](#inputs)
- [Dependencies](#dependencies)
- [Links](#links)
## Documentation
[Complete documentation is hosted at Read the Docs](https://hecatomb.readthedocs.io)
## Citation
[Hecatomb is currently on BioRxiv!](https://www.biorxiv.org/content/10.1101/2022.05.15.492003v1)
## Quick start guide
### Install Hecatomb
__option 1: PIP__
```bash
# Optional: create a virtual with conda or venv
conda create -n hecatomb python=3.10
# activate
conda activte hecatomb
# Install
pip install hecatomb
```
__option 2: Conda__
```bash
# Create the conda env and install hecatomb in one step
conda create -n hecatomb -c conda-forge -c bioconda hecatomb
# activate
conda activate hecatomb
```
__Check installation__
```bash
hecatomb --help
```
### Install databases and envs
__Download the databases__
```bash
# 8 threads = 8 downloads at a time
hecatomb install --threads 8
```
__Optional: prebuild envs__
These are automatically built when running hecatomb, but manually pre-building is useful if your cluster nodes are isolated from the internet.
```shell
hecatomb test build_envs
```
### Run test dataset
```bash
# locally: using 32 threads and 64 GB RAM by default
hecatomb test --threads 32
# HPC: using a profile named 'slurm'
hecatomb test --profile slurm
```
### Snakemake profiles (for running on HPCs)
Hecatomb is powered by [Snakemake](https://snakemake.readthedocs.io/en/stable/#) and greatly benefits from the use of
Snakemake profiles for HPC Clusters.
[More information and example for setting up Snakemake profiles for Hecatomb in the documentation](https://hecatomb.readthedocs.io/en/latest/profiles/).
__NOTE: Hecatomb currently uses Snakemake version 7.
The recent version 8 for Snakemake has some breaking changes, including some changes to the command line interface for cluster execution.
Any new Snakemake v8 profiles might not work with Hecatomb.
Please open an issue if you need help setting up a profile.__
## Inputs
### Parsing samples with `--reads`
You can pass either a directory of reads or a TSV file to `--reads`.
Note that Hecatomb expects paired read file names to include common R1/R2 tags.
- __Directory:__ Hecatomb will infer sample names and various R1/2 tag combinations from the filenames.
- __TSV file:__ Hecatomb expects 2 or 3 columns, with column 1 being the sample name and columns 2 and 3 the reads files.
[More information and examples are available here](https://gist.github.com/beardymcjohnface/bb161ba04ae1042299f48a4849e917c8#file-readme-md)
### Lonread support `--longreads`
Pass the `--longreads` argument to tell Hecatomb that you are using longreads.
### Library preprocessing with `--trim`
Hecatomb uses [Trimnami](https://github.com/beardymcjohnface/Trimnami) for read trimming which supports many different
trimming methods. Current options are `fastp` (default), `prinseq`, `roundAB`, `filtlong` (for longreads),
`cutadapt` (FASTA input), and `notrim` (skip trimming). See Trimnami's documentation for more information.
### Configuration
You can configure advanced parameters for Hecatomb.
Copy the default config: `hecatomb config`.
Edit the config file in your favourite text editor: `nano hecatomb.out/hecatomb.config.yaml`.
## Dependencies
The only dependency you need to get up and running with Hecatomb is [conda](https://docs.conda.io/en/latest/) or
the python package manager [pip](https://pypi.org/project/pip/).
Hecatomb relies on [conda](https://docs.conda.io/en/latest/) to ensure portability and ease of installation of its dependencies.
All of Hecatomb's dependencies are installed during installation or runtime, so you don't have to worry about a thing!
## Links
[Hecatomb @ PyPI](https://pypi.org/project/hecatomb/)
[Hecatomb @ bioconda](https://bioconda.github.io/recipes/hecatomb/README.html)
[Hecatomb @ bio.tools](https://bio.tools/hecatomb)
[Hecatomb @ WorkflowHub](https://workflowhub.eu/workflows/235)
[Hecatomb RRID:SCR_025002](https://scicrunch.org/resources/data/record/nlx_144509-1/SCR_025002/resolver)
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"description": "\n\n[](https://github.com/beardymcjohnface/Snaketool)\n\n\n[](https://hecatomb.readthedocs.io/en/latest/?badge=latest)\n[](http://bioconda.github.io/recipes/hecatomb/README.html)\n\n[](https://pypi.org/project/hecatomb/)\n[](https://github.com/shandley/hecatomb/actions/workflows/unit-tests.yaml)\n[](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 is currently on BioRxiv!](https://www.biorxiv.org/content/10.1101/2022.05.15.492003v1)\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. 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