Lambda

Introduction

Lambda is a local aligner optimized for many query sequences and searches in protein space.

For more information, please check its website: https://biocontainers.pro/tools/lambda and its home page: http://seqan.github.io/lambda/.

Versions

  • 2.0.0

Commands

  • lambda2

Module

You can load the modules by:

module load biocontainers
module load lambda

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 Lambda on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=lambda
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers lambda

lambda2 mkindexp -d uniprot_sprot.fasta

lambda2 searchp \
    -q proteins.fasta \
    -i uniprot_sprot.fasta.lambda