ORSON: workflow for prOteome and tRanScriptome functiOnal aNnotation.

Introduction

ORSON combine state-of-the-art tools for annotation processes within a Nextflow pipeline: sequence similarity search (PLAST, BLAST or Diamond), functional annotation retrieval (BeeDeeM) and functional prediction (InterProScan). When required, BUSCO completness evaluation and eggNOG Orthogroup annotation can be activated. While ORSON results can be analyzed through the command-line, it also offers the possibility to be compatible with BlastViewer or Blast2GO graphical tools.

The ORSON pipeline can run tasks across multiple compute infrastructures in a very portable manner. It comes with singularity containers making installation trivial and results highly reproducible.

Quick Start

i. Install nextflow

ii. Install Singularity for full pipeline reproducibility

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

nextflow run main.nf -profile test,singularity

To use this workflow on a computing cluster, it is necessary to provide a configuration file for your system. For some institutes, this one already exists and is referenced on nf-core/configs. If so, you can simply download your institute custom config file and simply use -c <institute_config_file> in your command. This will enable either docker or singularity and set the appropriate execution settings for your local compute environment.

iv. Start running your own analysis!

nextflow run main.nf -profile custom,singularity [-c <institute_config_file>]

See usage docs for a complete description of all of the options available when running the pipeline.

Documentation

This workflow comes with documentation about the pipeline, found in the docs/ directory:

1. Introduction
2. Pipeline installation
   • Local installation
   • Adding your own system config
3. Running the pipeline
4. Output and how to interpret the results
5. Troubleshooting

Here is an overview of the many steps available in orson pipeline:

Requirements

To use ORSON, all tools are automatically installed via pre-built singularity images available at SeBiMER ftp; these images are built from recipes available here.

Databases are also automatically download according to user's choice (default: Enzyme, UniProt SwissProt). See the Installing annotated sequence banks section of the usage documentation.

However, you must have local access to the BUSCO lineage databases. To download them, please refer to the tool's documentation to download the lineage databases

Credits

ORSON is written by SeBiMER, the Bioinformatics Core Facility of IFREMER.

Contributions

We welcome contributions to the pipeline. If such case you can do one of the following:

• Use issues to submit your questions
• Fork the project, do your developments and submit a pull request
• Contact us (see email below)

Support

For further information or help, don't hesitate to get in touch with the orson developpers: