Clever-toolkit

Introduction

Clever-toolkit is a collection of tools to discover and genotype structural variations in genomes from paired-end sequencing reads. The main software is written in C++ with some auxiliary scripts in Python.

For more information, please check:
BioContainers: https://biocontainers.pro/tools/clever-toolkit
Home page: https://bitbucket.org/tobiasmarschall/clever-toolkit/src/master/

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster

Version(s)

ANVIL

2.4

BELL

2.4

GAUTSCHI

2.4

NEGISHI

2.4

SCHOLAR

2.4

Commands

  • clever

  • laser

  • bam-to-alignment-priors

  • split-priors-by-chromosome

  • clever-core

  • postprocess-predictions

  • evaluate-sv-predictions

  • split-reads

  • laser-core

  • laser-recalibrate

  • genotyper

  • insert-length-histogram

  • add-score-tags-to-bam

  • bam2fastq

  • remove-redundant-variations

  • precompute-distributions

  • extract-bad-reads

  • filter-variations

  • merge-to-vcf

  • multiline-to-xa

  • filter-bam

  • read-group-stats

Module

You can load the modules by:

module load biocontainers
module load clever-toolkit

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 clever-toolkit on our clusters:

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

module --force purge
module biocontainers clever-toolkit

# Your clever-toolkit workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=clever-toolkit
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers clever-toolkit

# Your clever-toolkit workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=clever-toolkit
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers clever-toolkit

# Your clever-toolkit workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=clever-toolkit
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers clever-toolkit

# Your clever-toolkit workflow...

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

module --force purge
module biocontainers clever-toolkit

# Your clever-toolkit workflow...