Cactus

Introduction

Cactus is a reference-free whole-genome multiple alignment program.

For more information, please check:

BioContainers: https://biocontainers.pro/tools/cactus

Home page: https://github.com/ComparativeGenomicsToolkit/cactus

Note

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

Versions

Cluster	Version(s)
ANVIL	2.0.5, 2.2.3-gpu, 2.2.1, 2.2.3, 2.4.0, 2.4.0-gpu, 2.5.2-gpu, 2.5.2, 2.6.5-gpu, 2.6.5
BELL	2.0.5, 2.2.1, 2.2.3, 2.4.0, 2.5.2, 2.6.5
GAUTSCHI	2.0.5, 2.2.1, 2.2.3, 2.4.0, 2.5.2, 2.6.5
GILBRETH	2.2.3-gpu, 2.4.0-gpu
NEGISHI	2.0.5, 2.2.1, 2.2.3, 2.4.0, 2.5.2, 2.6.5
SCHOLAR	2.0.5, 2.2.3-gpu, 2.2.1, 2.2.3, 2.4.0, 2.4.0-gpu, 2.5.2-gpu, 2.5.2, 2.6.5-gpu, 2.6.5

Commands

• cactus

• cactus-align

• cactus-align-batch

• cactus-blast

• cactus-graphmap

• cactus-graphmap-join

• cactus-graphmap-split

• cactus-minigraph

• cactus-prepare

• cactus-prepare-toil

• cactus-preprocess

• cactus-refmap

• cactus2hal-stitch.sh

• cactus2hal.py

• cactusAPITests

• cactus_analyseAssembly

• cactus_barTests

• cactus_batch_mergeChunks

• cactus_chain

• cactus_consolidated

• cactus_covered_intervals

• cactus_fasta_fragments.py

• cactus_fasta_softmask_intervals.py

• cactus_filterSmallFastaSequences.py

• cactus_halGeneratorTests

• cactus_local_alignment.py

• cactus_makeAlphaNumericHeaders.py

• cactus_softmask2hardmask

Module

You can load the modules by:

module load biocontainers
module load cactus

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 cactus on our clusters:

Anvil

#!/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=cactus
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers cactus

# Your cactus workflow...

Bell, Gautschi, or Negishi

#!/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=cactus
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers cactus

# Your cactus workflow...

Gautschi-AI

#!/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=cactus
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers cactus

# Your cactus workflow...

Gilbreth

#!/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=cactus
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers cactus

# Your cactus workflow...

Scholar

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

module --force purge
module biocontainers cactus

# Your cactus workflow...