https://github.com/adamrtalbot/nf-chai

Nextflow pipeline to run the Chai-1, SOTA model for biomolecular structure prediction

https://github.com/adamrtalbot/nf-chai

Repository

Nextflow pipeline to run the Chai-1, SOTA model for biomolecular structure prediction

https://github.com/adamrtalbot/nf-chai/blob/main/

# nf-chai

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## Introduction

**nf-chai** is a bioinformatics pipeline for running the [Chai-1](https://github.com/chaidiscovery/chai-lab) protein prediction algorithm on an input set of protein sequences in FASTA format. The pipeline has been written in Nextflow to generate results for downstream analysis in a reproducible, scalable and portable way.

## Usage

> [!NOTE]
> If you are new to Nextflow, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.

First, prepare a FASTA file with your protein sequence(s) that looks as follows:

`protein_sequences.fa`:

```txt
>protein|name=short-protein-example
AIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPS
```

Now, you can run the pipeline using:

```bash
nextflow run seqeralabs/nf-chai \
   -profile  \
   --input protein_sequences.fa \
   --outdir 
```

## Credits

seqeralabs/nf-chai was originally written by the Seqera Team.

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

## Contributions and Support

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

## Citations

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

This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/main/LICENSE).

> **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).

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