SortMeRNA
SortMeRNA is a local sequence alignment tool for filtering, mapping and clustering ribosomal RNA (rRNA) from metatranscriptomic and metagenomic data. It is commonly used to separate rRNA reads from the rest of an RNA-seq dataset.
License
Free to use and open source under GNU LGPLv3.
Available
- Roihu: 7.0.0, via the
bio-appsmodule.
Usage
SortMeRNA is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the SortMeRNA module:
Databases
SortMeRNA needs one or more rRNA reference databases (FASTA files, such as the SILVA or Rfam rRNA sets), which are not bundled with the module.
Shared reference databases
CSC plans to provide shared reference databases at a central location on Roihu.
This is still being set up. Until it is available, download the rRNA reference
databases you need to a writable location (for example your project's /scratch).
Running SortMeRNA
#!/bin/bash
#SBATCH --job-name=sortmerna
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=04:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=4G
module load bio-apps/v202603
module load sortmerna/7.0.0
sortmerna --ref rRNA_db.fasta --reads reads.fq.gz \
--workdir sortmerna_run --threads $SLURM_CPUS_PER_TASK
Replace <project> with your CSC project (for example project_2001234).
See creating a batch job script for Roihu for more information about running batch jobs.