Metacompore is a snakemake pipeline running multiple RNA modifications detection tools for nanopore directRNA sequencing
At the moment MetaCompore supports the following tools:
- NanoCompore v1.03 :https://github.com/tleonardi/nanocompore/
- Epinano v1.02: https://github.com/enovoa/EpiNano
- Eligos2 v2.0.0: https://gitlab.com/piroonj/eligos2
- Tombo v1.5.1: https://github.com/nanoporetech/tombo
- MINES: https://github.com/YeoLab/MINES
- differr_nanopore_DRS: https://github.com/bartongroup/differr_nanopore_DRS
- Adrien Leger (@a-slide)
- Tommaso Leonardi (@tleonardi)
Clone the last tarball archive of the pipeline to your local system, into the location where you want to perform the data analysis
wget https://github.com/a-slide/MetaCompore/releases/download/0.1.3/MetaCompore.tar.gz
tar xzf MetaCompore.tar.gz
cd MetaCompore
If required, install singularity following the official documentation: https://sylabs.io/guides/3.7/user-guide/quick_start.html
Install miniconda following the official documentation: https://docs.conda.io/en/latest/miniconda.html
you can also install mamba to speed up snakemake installation: https://github.com/mamba-org/mamba
Create a virtual environment containing snakemake with conda
conda env create -f environment.yaml
You can also use mamba which will give you the same result, but much faster
mamba env create -f environment.yaml
Configure the workflow according to your needs by editing the files config.yaml
to configure the workflow execution
nano config.yaml
Edit the samples.tsv
to specify your sample setup and fast5 source files
nano samples.tsv
Activate the conda environment:
conda activate snakemake
snakemake --use-singularity -j 4
Set an LSF cluster profile https://github.com/Snakemake-Profiles/lsf
Edit the lsf rule specific config file lsf.yaml
Please be aware that MetaCompore is a research package that is still under development.
It was tested under Linux Ubuntu 16.04 and in an HPC environment running under Red Hat Enterprise 7.1.
Thank you
Adrien Leger & Tommaso Leonardi. (2021, April 28). MetaCompore. Zenodo. http://doi.org/10.5281/zenodo.4726171
MIT (https://mit-license.org/)
Copyright © 2020 Adrien Leger
- Adrien Leger / contact@adrienleger.com / https://adrienleger.com