Uniform analysis of coronavirus and SARS-COV-2 nanopore direct RNA sequencing datasets using MasterOfPores

This resource a joint effort, built by the team of the Epitranscriptomics and RNA Dynamics Lab (Novoa Lab) and the Bioinformatics Core Facility (BioCore) at the CRG.

We are very grateful to all researchers who have made their FAST5 raw direct RNA sequencing data available prior to publication, which nurtures this resource.

Note: (If you have only made FASTQ available, we can help you to make public your FAST5 data, which is needed to nurture this resource).

Goal of this resource

Given the world-wide reach of SARS-COV-2, we aim to facilitate access of the community to uniformly processed SARS-COV-2 nanopore direct RNA sequencing datasets. To this end, we have processed all publicly available dRNAseq datasets of coronavirus and SARS-COV-2 using our workflow MasterOfPores.

Please do contribute to improve this resource (code and/or data) - this is an effort done by the community for the community!

Accessing the processed data

You can access the processed data (base-called FAST5, BAM, per-gene counts, RNA modification predictions, polyA tail length estimations) by clicking the links of each Sample in the tables shown below

What is MasterOfPores?

MasterOfPores is a Nextflow framework for the analysis of nanopore direct RNA sequencing data.

The MasterOfPores workflow includes all steps needed to process raw FAST5 files produced by Nanopore direct RNA sequencing into mapped BAMS, per-gene counts, polyA tail estimations and RNA modification predictions.

The pipeline currently consists of 3 modules:

  • Module 1: NanoPreprocess. Performs base-calling, demultiplexing, quality-filtering, mapping, per-gene/per-transcript counting, mapping and reporting (HTML MultiQC report)
  • Module 2: NanoMod. Prediction of RNA modifications
  • Module 3: NanoTail. Prediction of polyA tail length estimations

Please see more details about MasterOfPores in our recently published manuscript here.

You can also check MasterOfPores documentation here.