sortmerna
Link to section 'Introduction' of 'sortmerna' Introduction
SortMeRNA is a local sequence alignment tool for filtering, mapping and clustering.
For more information, please check its website: https://biocontainers.pro/tools/sortmerna and its home page on Github.
Link to section 'Versions' of 'sortmerna' Versions
- 2.1b
- 4.3.4
Link to section 'Commands' of 'sortmerna' Commands
- sortmerna
Link to section 'Module' of 'sortmerna' Module
You can load the modules by:
module load biocontainers
module load sortmerna
Link to section 'Example job' of 'sortmerna' Example job
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
To run SortMeRNA on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=sortmerna
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers sortmerna
sortmerna --ref silva-bac-16s-id90.fasta,silva-bac-16s-db \
--reads set2_environmental_study_550_amplicon.fasta \
--fastx --aligned Test