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.

Versions

• 2.2.0

Commands

• lima

Module

You can load the modules by:

module load biocontainers
module load lima

Example job

Warning

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