nf-chai is a 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.
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 your protein sequence(s) that looks as follows:
protein_sequences.fa:
>protein|name=short-protein-example
AIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSNow, you can run the pipeline using:
nextflow run seqeralabs/nf-chai \
-profile <docker/singularity> \
--input protein_sequences.fa \
--outdir <OUTDIR>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:
If you would like to contribute to this pipeline, please see the contributing guidelines.
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.