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hecatomb is a virome analysis pipeline for analysis of Illumina sequence data

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---

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: an integrated software platform for viral metagenomics__,
_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_,
GigaScience, Volume 13, 2024, giae020, [https://doi.org/10.1093/gigascience/giae020](https://doi.org/10.1093/gigascience/giae020)

## 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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