lima
Link to section 'Introduction' of 'lima' Introduction
Lima is the standard tool to identify barcode and primer sequences in PacBio single-molecule sequencing data.
For more information, please check its website: https://biocontainers.pro/tools/lima and its home page: https://lima.how.
Link to section 'Versions' of 'lima' Versions
- 2.2.0
Link to section 'Commands' of 'lima' Commands
- lima
Link to section 'Module' of 'lima' Module
You can load the modules by:
module load biocontainers
module load lima
Link to section 'Example job' of 'lima' 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 Lima on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 12
#SBATCH --job-name=lima
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers lima
lima --version
lima --isoseq --dump-clips \
--peek-guess -j 12 \
alz.ccs.bam primers.fasta \
alz.demult.bam