modr 🔬

An Oxford Nanopore direct RNA-sequencing Pipeline

This is the home of the pipeline, modr. Its long-term goals: to accurately estimate known and novel transcript expression, to predict poly-A tail lengths, and to detect RNA modifications in Oxford Nanopore direct RNA-sequencing data like no pipeline before!

Overview¶

Welcome to modr's documentation! This guide is the main source of documentation for users that are getting started with the ONT RNA modification pipeline.

The ./modr pipeline is composed several inter-related sub commands to setup and run the pipeline across different systems. Each of the available sub commands perform different functions:

modr run
Run the modr pipeline with your input files.

modr unlock
Unlocks a previous runs output directory.

modr install
Download remote reference files locally.

modr cache
Cache remote software containers locally.

modr is an awesome pipeline to detect known/novel transcript expression, poly-A tail lengths, and RNA-editing in Oxford Nanopore direct RNA sequencing data. It relies on technologies like Singularity¹ to maintain the highest-level of reproducibility. The pipeline consists of a series of data processing and quality-control steps orchestrated by Snakemake², a flexible and scalable workflow management system, to submit jobs to a cluster.

The pipeline is compatible with direct RNA-sequencing data generated from Oxford Nanopore sequencing Technologies. As input, it accepts a set of FastQ & Fast5 files and can be run locally on a compute instance or on-premise using a cluster. A user can define the method or mode of execution. The pipeline can submit jobs to a cluster using a job scheduler like SLURM (more coming soon!). A hybrid approach ensures the pipeline is accessible to all users.

Before getting started, we highly recommend reading through the usage section of each available sub command.

For more information about issues or trouble-shooting a problem, please checkout our FAQ prior to opening an issue on Github.

Contribute¶

This site is a living document, created for and by members like you. modr is maintained by the members of OpenOmics and is improved by continous feedback! We encourage you to contribute new content and make improvements to existing content via pull request to our GitHub repository .

References¶

^{1. Kurtzer GM, Sochat V, Bauer MW (2017). Singularity: Scientific containers for mobility of compute. PLoS ONE 12(5): e0177459.}
^{2. Koster, J. and S. Rahmann (2018). "Snakemake-a scalable bioinformatics workflow engine." Bioinformatics 34(20): 3600.}

Last update: 2024-02-06