nf-chai

POC implementation of Chai-1 in Nextflow

Introduction

nf-chai is a simple, proof-of-concept bioinformatics pipeline for running the Chai-1 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 on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

First, prepare a FASTA file with entities supported by Chai-1 in the format highlighted below. You can also provide a directory with multiple FASTA files by specifying the --input parameter with a directory path like this: --input "/path/to/fasta_files/*.fasta|*.fa".

multiple_entities.fa:

```txt

protein|name=example-of-long-protein AGSHSMRYFSTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASPRGEPRAPWVEQEGPEYWDRETQKYKRQAQTDRVSLRNLRGYYNQSEAGSHTLQWMFGCDLGPDGRLLRGYDQSAYDGKDYIALNEDLRSWTAADTAAQITQRKWEAAREAEQRRAYLEGTCVEWLRRYLENGKETLQRAEHPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQWDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGEEQRYTCHVQHEGLPEPLTLRWEP protein|name=example-of-short-protein AIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM protein|name=example-peptide GAAL ligand|name=example-ligand-as-smiles CCCCCCCCCCCCCC(=O)O ```

Run the pipeline using CPUs with the command below:

bash nextflow run seqeralabs/nf-chai \ --input multiple_entities.fa \ --outdir <OUTDIR> \ -profile <docker/singularity>

Run the pipeline using GPUs with the command below:

bash nextflow run seqeralabs/nf-chai \ --input multiple_entities.fa \ --outdir <OUTDIR> \ --use_gpus \ -profile <docker/singularity>

Set the --weights_dir parameter to a location with the pre-downloaded weights required by Chai-1 to avoid having to download them every time you run the pipeline.

To further improve prediction performance using pre-built multiple sequence alignments (MSA) with evolutionary information, set the --msa_dir parameter to a location with *.aligned.pqt format as required by Chai-1.

Credits

nf-chai was originally written by the Seqera Team.

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

Citations

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT 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.