genomeannotator

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genomeannotator

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Pipeline for the identification of (coding) gene structures in draft genomes.

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## Introduction

**nf-core/genomeannotator** is a bioinformatics best-practice analysis pipeline for the annotation of eukaryote genomes. It was developed with a focus on metazoans - although other groups should work as well.

The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!

## Pipeline summary

1. Preprocess assembly (filter out small contigs, clean sequence names)
2. Align evidences (proteins, transcripts, RNAseq)
3. Convert alignments to annotation support
4. Build gene models using [AUGUSTUS](https://github.com/Gaius-Augustus/Augustus) and optionally [PASA](https://github.com/PASApipeline/PASApipeline)
5. Compute consensus gene build using [EvidenceModeler](https://evidencemodeler.github.io/)

Optional steps include de-novo transcriptome assembly ([Trinity](https://github.com/trinityrnaseq/trinityrnaseq)) and annotation mapping from related genomes ([Satsuma2](https://github.com/bioinfologics/satsuma2) and [Kraken](https://github.com/GrabherrGroup/kraken)).

## Quick Start

1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.10.3`)

2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(please only use [`Conda`](https://conda.io/miniconda.html) as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_

3. Download the pipeline and test it on a minimal dataset with a single command:

```console
    nextflow run nf-core/genomeannotator -profile test,YOURPROFILE --outdir <OUTDIR>
    ```

Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string.

> * The pipeline comes with config profiles called `docker`, `singularity`, `podman`, `shifter`, `charliecloud` and `conda` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`.
    > * Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile <institute>` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.
    > * If you are using `singularity`, please use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs.
    > * If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs.

4. Start running your own analysis!

```console
    nextflow run nf-core/genomeannotator --input samplesheet.csv --outdir <OUTDIR> --genome GRCh37 -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
    ```

## Documentation

The nf-core/genomeannotator pipeline comes with documentation about the pipeline [usage](https://nf-co.re/genomeannotator/usage), [parameters](https://nf-co.re/genomeannotator/parameters) and [output](https://nf-co.re/genomeannotator/output).

## Credits

nf-core/genomeannotator was originally written by Marc P. Hoeppner.

We thank the following people for their extensive assistance in the development of this pipeline:

Montserrat Torres-Oliva (@MontseTor)

## Contributions and Support

If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).

For further information or help, don't hesitate to get in touch on the [Slack `#genomeannotator` channel](https://nfcore.slack.com/channels/genomeannotator) (you can join with [this invite](https://nf-co.re/join/slack)).

## Citations

An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.

You can cite the `nf-core` publication as follows:

> **The nf-core framework for community-curated bioinformatics pipelines.**
>
> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
>
> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).

genomeannotator

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